I have to say I like.
The Rak'Gol are one of my favourite bits of Rogue Trader - a genuinely new, fairly unique race of generic evil dudes, with - as noted - a very Firefly 'reavers' feel to them.
Thoughts and suggestions:
Whilst the orks are an easy starting point, Rak'Gol aren't disorganised; there's no reason for the reduced leadership, for example, or the auto-AAF - which is in part there because of the reduced leadership.
The overpowered drives thing is a key part of what makes them Rak'Gol.
I like the idea of placing blast markers to represent the trail of radiation, but my main concern is the idea that it becomes easy to 'blast marker bomb' a ship, like people sometimes do with tyranid drone spore cysts. Besides which, it's a continuous output rather than a 'splot' every so often.
If it was me, I'd suggest the following:
1) Firing at a Rak'Gol ship from behind counts as firing through a blast marker
2) If a Rak'Gol ship suffers an Engine Room Damaged critical hit, it suffers two points of extra damage rather than one
3) If a Rak'Gol ship is destroyed by a Plasma Drive Overload catastrophic damage, roll 4d6 rather than 3d6 for the blast radius.
Howler batteries are, as noted, high Rate Of Fire. This makes them especially effective vs escort craft and ordnance - where filling space with shells is more important than the power of an individual weapon.
One way to represent this preference for lighter ships, without giving them ridiculous firepower, would be to treat escorts as capital ships when calculating how many hits to roll for on the gunnery table.
The effectiveness against ordnance can just be incorporated into the turrets stat (which should be high)