You guys want the ND V8 
You don't know it yet, but good lord is it good. I really, really love the way the ND is coming together, but it's waaay out of budget so it's not part of this discussion.
Monster still makes Ford swap parts, but I do think the LSx is the better choice for power density, compatibility with the stock geometry, ground clearance and parts availability. But not for sound, alas.
The newer the car, the easier the swap is from a mechanical standpoint. The NB has a leetle tiny bit more room in the engine bay and an electronic speedo. The NC has even more room with very little cutting (but more subframe reinforcement).
The newer the car, the more refined the end result as well. On the NA and NB, you never forget you're sharing a little car with a big engine. It's more of a hot rod feel. The NC has more of a GT vibe, it's got better isolation. But it also feels bigger and loses a bit of sharpness on track.
One thing people forget about the pop-up headlights is that they use standard 7" rounds. Loads of very functional upgrade options for those. 1999-00 headlights are pretty poor. 2001-05 are much better. NC are okay but have no upgrade path.
CAN isn't much of an issue with the magic box we have from MRS electronics. We haven't started NC development yet, but it should be fairly straightforward to keep the gauges working. We've already got PRHT and ABS sorted.
Regardless, I'd start with the car I wanted to finish with. If you like the looks of the NB, build an NB. It's the most popular platform right now. The NC PRHT is a staff favorite at FM because it's such a guilty pleasure, so easy. It works well on track too, although it feels bigger than the earlier cars and roll protection is an issue. But if you like the NB better, get the NB.
For LS3 crate engines, there are three choices.
Stock (aka the 430). This has stock manners. A fairly quiet purr at idle, very smooth, excellent street behavior.
E-ROD. Same engine but with more emissions monitoring. This is handy if you have emissions tests - it has rear O2 sensors, for example. There's no difference in actual emissions, but it gives more info.
LS376/480. Obsolete thanks to the..
LS376/525. This is the crazy version. Rump rump rump idle, razor-sharp throttle response and extra power up top. It's got about 40-50 more hp at the wheels and feels just nuts. I love this engine. It's got such an edge to it.
Engine management: get the GMPP kit for the 430. Same hardware is used with the 525 but it's more expensive there. Just change out the tune.
Alternately, you could adapt a harness and PCM from a factory car. It's well documented and pretty clean.
Trans is a T56, no question. Best option is the Magnum for better shifting and strength. You won't find this used in the wild as it's not an OE fitment so it's a judgement call as to whether the improvement in shift quality is worth the premium. We have found these transmissions are sensitive to fluid choice. As with so many aspects of these engines, GM got it right and the aftermarket struggles. Use a stock LS7 clutch.
Rear end, go with Camaro. Available as a kit for the NC, it'll probably be a kit for the NA/NB by the time you build it. The Ford 8.8 is big and heavy and the GM parts are surprisingly cheap new. IIRC you're looking for a 3.4 or so.
This page gives you a list of everything we use in a conversion. It's a good guide on what you'll need to address, even if you plan to DIY most of it.
All of our V8 cars are expected to be able to roll up to the track and perform. The biggest thing you need to deal with is brakes, these cars are hard on brakes due to the velocity involved.
