After quickly reading the thread I came up with some thoughts. Some of these might have been said allready but there was lot of posts.
Story: The system or systems have surrouned by a Warp Storms, making long Warp Jumps to other Imperial systems impossible. The Scenario then involves the factions trapped inside the Warp Storm area to fight for their survival. A Warp Storm can last for hours up to milliena so there is no time line to follow.
2D vs 3D: The BFG Tabletop game is in 2D, this doesn't mean that a computer game has to be that but it allready fits so well with the Sins engine that I don't see a reason to change it.
Races: I would begin with making the "basic" races. Aka, Imperial Navy, Space Marines and Chaos. Even though Eldar is my favorite race and I play them myself in BFG I wouldn't start off trying to make them. Their ships are extremly powerful and behaves very diffrently from other races. I would go for Orcs, Tau and maybe Tyranids after the 3 first basic ones. Dark Eldar is the perfect pirat race, and their ships are more similar to the other "normal" ships of BFG.
Ships: The Ship classes in Sins is allready very fitting to the BFG setup with frigates, cruisers and cap ships. (Cap ships = Battleships in BFG). In BFG a singular Frigate isn't any real threat to a Cruisers or Battleship. But they can suprise a player with their quick speed, fast turn rate and maybe more importantly their combined firepower that quickly ramp up to be a deadly salvo even for great Battleships.
Torpedos: I would love to see them in a mod even though I know they might be difficult to actually create. Even though they go straight ahead in BFG (Unless you have spesial torpedos)you can make the guided in game. Not as guided as the missiles that are ingame, but so they atleast can turn towards the target. Maybe making them a class of ships that explode on impact? That way you could have fighters intercept them as they approach your fleet. My best idea for a technical solution for this would be:
1. Make them a "ship" that is a little faster that a normal fighter.
2. Give them a slow turn rate.
3. Give them a life timer, making them explode after X ammount of seconds.
Boarding Actions: I guess I would make this a spesial attack from ships that can only be used at close range. Depending on the system the coder or scripter can make it could damage anything from Hull, to Anti-Matter (Guess you will call this something else in your mod) to spesial abilites. Maybe even capturing enemy ships, even though it would Lore wise be impossible for orks to capture Eldar ships as they are unable to operate them. But orks do often capture imperial ships can re-fit them to make them orky.
Firepower, Shield, Abilites = Balance: If you get all the models in place, new code or scripts aswell this will still be the hard part I guess. Balance is in any game, and atleast in RTS games make or break. I think it's something that massive ammount of playing and testing will show though. But you will still need people that have the time to listen to the feedback and tweak each ship. It took Blizzard about 4 years or so make Star Craft balanced so it's not an easy job.
The last thing I would just like to say is this. Make it fun! What I mean about this is try and not get to caught up in what the BFG Rulebook says and don't say. Go with what you can make and try and get the most out of it. If you want an example of what I mean just play Dawn of War

. It's not like the tabletop game at all but it's fun and I think it really brings out a lot of the "attitude" from the Warhammer 40k world.
Great work on the models for those who have made those. I really really loved the Despoiler pictures. Atleast the one that show the siluett in front of the sun, made more sense that it wasn't any textures on it then

.