for what its worth......
Cable throttle definitely. You then have the option of using after-market traction control or just relying on the "brakes" part of the ABS-TC. In reality, I have the tc turned off in my Holden and rarely break traction.
For brakes, my Omega track-car uses ML front discs and Audi Q7 calipers, single piston jobbies that I believe are also fitted to some A4s and S4s. These are 365mm and seem to do the job all right. Subjectively, they're better than the Holdens APs. I haven't updated the rears, but do remember that the car never has any rear load - it rides at 332kg on each rear wheel ( as opposed to 450 or so on the front )
My Holden GTS is lighter than my Omega MV6
Check out Saab 9-5 rear discs. The main problem you have is the wheel stud pcd. whilst the ML setup is compatible at 112mm pcd, on the rear you need matching pcd and handbrake drum diameter. The Holden uses a larger handbrake drum than Omega B
The "standard" Holden (non-AP) brakes are absolutely shocking. Maybe the only car I've driven with worse brakes than Omega B.
Yes, you'll need to move the ABS modulator "block", but that's no problem. On the Holden, the engine ecu llives there - yes right next to the exhaust manifold.
Front-mounted rack, although a great idea for handling, isn't easy. You need to swap over the struts from left to right and I haven't gotten my head around that just yet. The rear rack ( that I have of yours ) will work with the subframe, but could give some exciting lower column u/j angles, but that'll need to be done "on the car".
The BTR diff can be made to fit the rear subframe, but you're probably better off starting with an Omega A rear subframe. I have a hunch that the standard diff and driveshafts will be ok so long as you don't go drag-racing.
The shell will live without the gearbox mounting, but I'd replace the same amount of strength with the mount system that you eventually use.
From your photos, the header situation isn't too bad