Nice to see it on the road,

more than either of mine are atm
Scorpion has been the default for many but is well known to be a bit on the obnoxious side. I'm sure a decent place would swap one or both boxes to tone it down without chucking the whole thing?
The 3.64 diff you have seen will be fine, the small case probably wouldn't last long anyway, mine didn't. The GS37BZ box suggested in the comments is also from the M54B30 FL E46 330i. Good box but would not solve the problem of the diff. 5-speed with the 3.64 would be fine. 6-speed only comes into its own with longer diff ratios. I am planning to use that box with a torsen 3.15. (exactly as the OEM Z3 was setup) That gives a cruising gear but keeps a decent spacing further down.
The Bilstein B12 kit (B8 dampers and Eibach springs) were tried and tested to be the most you would want for daily. I had similar Koni yellows and had no issue. Coilovers can be hit and miss and often price doesn't guarantee quality. Not cheap but the KW V3 can alter slow (cornering) bump independently of fast (pothole) and rides well for a performance coilover.
I'd go OEM rubber most joints. BMW knew what thy were doing for a few things
I put over 100k miles on my 323i but back then we knew no different and other options were worse. Going end to end of the country is a different proposition in cars now.
Getting things to how you want them is part of the 'fun' and you don't know what works until you have tried it.
Good luck with it!
