I'll go one at a time on your questions.
T-56 vs CD009
Size: they weigh almost the same, and both will necessitate removing the original mounting ears from the tunnel. Assuming the rear of the engine is in the same place as an L-series, you'll need a shifter relocate for the CD009. I think if you get the F-body version of the T-56, the shifter lines up nicely. That's what TimZ did with his T-56 behind an L.
https://forums.hybridz.org/topic/126809-t56-behind-an-l-series/
Drivability: I've never driven a car with either of these trans, though I do have a kit waiting to put a CD009 in my car. If you're worried more about twisty roads and the track, I would lean towards the CD. 1st gear in the CD and 6th in the T-56 will likely both be useless in those cases, so you're basically comparing 1-5 of the T-56 and 2-6 of the CD. The CD has closer ratios over that span, but really what you want will be track/road dependent. The gears you use the most and the shifts you make the most would likely inform which one will be preferable.
Diffs
5-600hp is a lot. The R200LN has a history of being able to handle that, but keeping it almost definitely means keeping the stock stub axles and drive axles, which are the weak points of the stock setup. You might be fine if you're just on road courses, but at 600hp I'd be a little worried about a stub axle snapping and your wheel departing the car.
The R200SN and 8.8 conversions are both strong and easy to do. I'm in the process of putting an R200SN into my car with a swap kit from T3, but if I had to start from scratch, I might lean towards the 8.8 for a track car. The kit is cheaper from https://invincibleextremes.com/ than anything to put in a short nose. The 8.8 is a bit heavier, but the parts availability is so much better for brakes and hubs. It's impossible to get some stuff new for the R200SN setup, and even good used parts can be hard to find, especially if you go with the Q45/Z32TT versions of the diff. Mustang parts can be bought new and will be available for a long, long time.