Excellent.
Notes as I'm reading:
p18, Col3, Types: Normally a colon ":" is used to introduce lists, not a semi-colon ";".
p20, Holofield Breakout: Lock-On only applies to Scatter weapons? The way it's phrased right after rerolling Scatter makes it seem like that's the only thing it affects. Is that intentional, or does Lock-On also cancel the Lance Penalty and/or Battery penalty? I know that lock on used to cancel the reroll for lances, but that was before the change over to penalties for range.
p21, Multiple Criticals: Probably needs to clarify if criticals roll over when a weapon system exists but is already damaged? e.g. If an Eldar Wraithship's keel weapons are already damaged by a critical, and another keel damage is rolled, does this simply mean both must be repaired to access keel weapons, or does the crit roll over to the next thing on the chart as if there were no keel weapon?
p21, Col 3, Effects of Hulks on battlefield: I've always found the rule that you cannot fire on friendly hulks strange. This is the grimdark of the 41st millenium. Shooting your (now ex-) comrades to destroy your enemies is the new hotness. Their heroic sacrifice to destroy the infidels/traitors/xenoscum will be honored by their gods/masters/demon/ancestors/descendants. Imperial Commissars encourage this sort of thinking all the time, Eldar forsaw the need, Tau accept it for the greater good, Orks and Chaos think its funny, Nids and Necrons probably don't even notice. I'd almost be inclined to make the inability to do this the exception, rather than the rule. Is there a compelling game balance reason that you should not be able to shoot at friendly hulks?
p23, Col 1, Fleet Ordnance Limits: Augmented Launch Facilities should be in bold for consistency.
p24, Hardy: Interesting, I like it.
p25, Col 2, Torpedo effects: suggest "on the facing hit" rather than "on the side hit". Side is a bit ambiguous, and facing is the technical term introduced elsewhere in the document.
p26, Col 2, CAP: Missing an E on Enemy.
p26, Col 2, Fighters vs Torpedoes et al: Interesting. I like the 2d3 mechanic, rather than simply wiping out the wave.
p26, Col 2, Fighters vs Bombers et al: Not sure I like this change as much; I can see how it would increase the attractiveness of mixed waves, but d3+1 and d3 seems pretty harsh. A single fighter on cap could potentially neuter an entire bomber wave of 4, even before turrets, which makes it seem to me that you now almost have to devote fighters to CAP, especially with the changes to bombers that get through. My gut reaction is that these values should probably be d3 bombers and d2 for fighter-hybrid types, especially given how many resilient fighter types there are out there.
p26, Col 3, Bombers vs Ships: The change to increase bomber damage is interesting. Likewise, I can see how this is trying to balance out the increased efficiency of fighter types vs the bombers. Not sure if the exact balance is right; has there been any significant playtesting with these values?
p27, Col 2, Fighter Boats: Fighter boats function as Fighter boats? I think is supposed to be 'behave as Fighters against'.
p27, Col 2-3, Torpedeo craft: Might be worth a note describing how waves work. I imagine you simply combine the strengths of each squadron in the wave, rather than producing individual salvoes of 2/1 for each point of strength in the wave. I do like the Torpedeo Fighter concept, though I'm not entirely sure which races would use such craft. The "Evil" trifecta of Orks, Chaos, and Dark Eldar seem most likely.
p27, Col 3, Mines: These seem really powerful, especially in fleets like most Eldar and Ork variants, where getting to within mine range is par for the course (either via armor or speed). I'm just imagining a Torture or Eclipse class dashing up behind an Emperor from over 40cm away and dumping a load of 4 mines out. Even with average rolling for both turrets and hits per wave, that's going to end up doing 3-4 direct hits, and if the 'halves' go for you instead of against you, that's around 7 hits (because a second mine sneaks through the turrets adding 3.5 more hits on average). And against a cruiser with only 2 turrets, instead of 5, that's going to be an average of 10 hits. Complete destruction of a Lunar or Murder in one attack, from an effective range beyond their weapons? Seems too good. Again, gut reaction without any play testing, but I'd be inclined to make these work like as to Lances as normal Torpedo and Bomber's are to Weapon Batteries. d6 attacks per remaining Strength, each of which inflicts a hit on a flat 4+, rather than using the armor value the way bombers and torpedoes do. That roughly halves the damage, meaning a typical line cruiser with 2 turrets is only going to take 5 hits from a wave of 4. Still enough to cripple (at the cost of having to get to within 10cm), but not outright destroy.
Random related thought: I can totally see some races, especially Orks and Nids, making Mine-Bombers (aka Kamikaze Bombas), loaded up with mines the same way a Torpedo Bomber drops torpedoes. Cram as much explosives onto their frame as you can and fly 'em straight into the enemy one way for "precision" delivery of huge booms.
p29, Col 1, Hit and Run: "Essentially causing a critical hit on the lower end of the table." This clause needs to be a sentence. "This will essentially cause a critical hit result from the lower half of the table", perhaps.
p30, Col 2, Numerical Superiority: This is awkwardly phrased. How about: "Larger squadrons are more likely to contain a veteran commander, whose experience can bolster the efficiency and morale of the entire squadron. Any squadron of Escorts or Orbitals which contains 5 or more members may re-roll the die when randomly determining Leadership for that squadron."
p30, Col 3, Ordained Duty: "Capital Ships, which expense" should be "whose expense", and in the following sentence, "Despite this" should probably be "Because of this" or "Due to this".
p32, Col 3, Shooting By Squadrons: When you say "identical" does this mean identical by type, or exactly identical? Could a squadron of a Dictator and Overlord combine their weapon batteries, even though they have different strengths?
p33, Col 3, Launching Ordnance: I don't like the change of mandating that only those ships in contact-chain with the Lead ship can benefit from this. Especially since the Numerical Superiority rule encourages larger squadrons. I should be able to form up into, say, a group of 3 and a group of 4 and have both groups benefit.
p36, Col 2, Placing Celestial Phenomena: It seems slightly counter-intuitive to me that fleets with aggressive attack ratings are more likely to be able to force conflicts in the further out regions. The math makes sense when you dissect it, but it just feels a little backwards.
p42, Col 1, Fighting in Low Orbit: This column cuts off mid sentence.
From the Section on Leadership on, the page numbers are clearly not fixed yet, as you mentioned, so I'll switch to referring to things by section/subsection.
Leadership, Starting Leadership, Col 2: Instead of "each race uses a different column to determine their resultant leadership score", I recommend "each race uses a particular column". Different implies no two races can use the same column, which is clearly not the case. I also recommend swapping columns 1 and 2 on the table, so that roughly speaking, the columns get better from left to right, just as the scores get better from top to bottom. I understand why they're set up the way they are (I being the "standard" table, while II is "bad" and III and IV are better than average), but since we're already divorcing the table from the fleet entries, you might as well make the table more consistent and adjust the numbers accordingly in the fleet entries.
Fleets of the 41st Millenium: Lots of this is replicated from Ship Types, The Fleet, Characters and other sections. The information here that I don't see in a newer section are the base sizes (which should probably go into Ship Types) and the rules for allies (Not sure where to put this, probably under The Fleet, but maybe not). Also, just as a general note, large flight bases are 60mm, not 50mm, as mentioned under Battleship and Grand Cruisers.
Armaments, Pulsar Lances: The wording on how this works feels cumbersome to me. Perhaps: "If a Pulsar Lance successfully hits, immediately roll a second attack. If the second attack successfully hits, roll a third and final attack. If the firing ship is on Lock On orders, only the first attack with each Pulsar Lance may be re-rolled".
Armaments, Crystal Lances: Streamline final sentence to "Crystal Lances have a hit rating of 5+ and the Rending quality".
Armaments, Zzap Guns: Either two separate sentences ("Zzap Guns have a hit rating of 4+. After firing a ZZap gun put a Blast Marker in base contact with the firing ship's rear arc") or streamline the single sentence ("Zzap Guns have a hit rating of 4+ and whenever a ship fires a Zzap gun, place a Blast Marker in contact with its base in the rear arc").
Armaments, Cutting Beam: the May at the top of the second column should not be capitalized. This whole entry is also unclear to me, especially without the context of the Fleet List to see how the strength is rated and how Demiurg ships collect Blast markers. I'll suggest something like "A Cutting Beam functions as a Lance weapon with one shot, no matter the Firepower Rating listed for the weapon entry, and may fire an additional 1 shot for each Blast Markers collected by the firing ship, up to the maximum Firepower Rating listed. For each extra shot generated, remove 1 Blast Marker from the pool held by that ship after firing." That should make it clear that the strength is dependant on a particular mechanic in the fleet list.
Armaments, Gravatic Hook: Hook Dependant looks like it should be a Special Quality, but is not (yet).
Special Qualities: Presumably the early qualities page (before the Armaments Section) is now out of date and should go.
Special Qualities, Transport: I'm loathe to tie the Inefficient Engines to Transport directly. Instead, I'd rather just have all transports get both if necessary. Mostly because I can forsee certain races who do not, in fact, have Inefficient Engines on their transports, either due to superior technology or the simple expedient of custom designing classes of ships with both warship class thrusters and transport capacity. And while I like the idea of tying Transport's capacity to the ship's remaining hull points, I again can imagine scenarios where a ship might have fewer initial transport points than hull points. Q-ships, for instance, might have the Transport quality at lower than regular levels, in order to account for their warship quality targeting systems and weapons. Such a ship might have 6 hull points, appearing like a typical largish transport, but only have 2 actually available transport slots (to further its guise as a merchant ship), with the other 4 being take up by damage control systems, launch bays, and lance batteries for killing daring pirate raiders. Likewise a ship meant for rapid insertion of ground troops might have 4 hull points, but only 1 or 2 points of transport, in order to mount the armor, shields, and engines of a capital ship, to protect it.
Special Qualities, Improved Auspex Array: Suggest renaming this to 'Improved Sensor Arrays'. Not all races will necessarily have Auspex as their sensor technologies.
Solar Sails: I like having this in the main book and in its own section. As a suggestion, when describing how they turn, I'd use the following phrasing: "If a vessel with Solar Sails wishes to turn, it may only do so at the beginning of either, or both, movements, but not during each movement as with normal engines." Also, as on the bottom of the first column where you summarise the movement rules, standard practice is to use colon to introduce a list, not a semi-colon.
As a somewhat random aside, it occurs to me that by making Solar Sails a quality, there's no reason a ship might not have both Solar Sails and normal engines, though no current ships do, obviously.
Overall, with the exception of the stuff that you haven't gotten to yet, things are looking pretty good. The only two things which leap out at me for game balance are Mines and the changes to Bombers/Fighters. I'm not opposed to the bomber change in principle (in fact, I like it and think that adding a reason for fighters is good), I just think the exact values need a little tweaking. Mines, OTOH, I think are just too good right now, especially for certain fleets.