I tried to get my Gen1 upgraded as I wanted to run coil on ignition. (More on that later...) So I feel your pain.
I use the BS3 Gen 1 box for my rev limiter and have the DIS4 setup. I've never had a misfire problem with my car either. It does seem to eat up coils more often with the DIS though.
I have mine wired so when the trans brake is engaged the two step is on and the nitrous is in-activated. When I release the transbrake (assuming the WOT switch for the N20 is closed) the two step drops off and the nitrous flows. I had to wire the relay for reverse polarity to accomplish this. In other words, grounding the trans brake button creates, opens the nitrous circuit (inactivating it), when the transbrake circuit opens, the nitrous circuit closes (activating it). I add this because you may have to do some trickery like this with your boost controller. Your boost controller will be indepent of the two step if you get an electronic one. Some people set the two step higher (which would create too much boost at launch -tires would spin) and then use the e-boost controller to limit boost. That way, there is some lag time between when you launch and the boost comes up. It makes a bit of a softer launch if your chassis can't handle all that power off the launch.
Now onto the coil on plug. Everyone likes the distributor right now. Instead, try the state of the art and order an LS1 BS3 box and use coil on plug. Better spark and you again have individual cyl. spark control (not so with a distributor) and NO chance of spark scatter. At some point, people will switch to this I suppose. I'm not sure why no-one has done it yet except that as far as I know, the BS3 is the only way to do it. XFI might but I simply don't know, I do know it's possible with the BS3. Now THAT would be the way to go. I'm currently watching eBay for some LS2 coils on the cheap. They are supposed to be better than even the MSD coils. Go on, blaze the trail !!
In the mean time, I'll just have to live with the waste spark... :frown: