The 5 speed worked fine. I switched the diff to a 3.23 out of a Z3M car to change the gearing. The 6 speed simply offers an overdrive and I doubt you are going to be interested in gas mileage if you are doing the swap. The 5 is simpler, cheaper ($200-400 vs >$1k), lighter and easier to source.
I thought about attempting the swap in my Bavaria, but for the cheap price of a newer M30 (M30B35) and a bolt on turbo from TCD, you can get more HP with a way simpler install. You would need to upgrade the fuel system on any swap to FI, so that is a wash. But the fab work needed for the mounts, exhaust, pan, wiring...etc, it just didn't seem worth it to me.
It would be cool, but what would you gain.
I also ran alpha-n. I always had a flat spot in the tune around 2-3k rpm. The difficulty with alpha-n is getting a tune that is specific to your climate, mods, etc. It did simplify the wiring though. If you are thinking about it for the E30, I can help with any questions you may have.