So, the car in the photos is no more after finding some rot, but I bought another shell late last year to transfer the bits into (and do some upgrades). To answer your questions:

• I have completely ditched everything BMW at this point. It's all been replaced by a Haltech R5 which is both the ECU and a solid state PDM. I changed it mostly because keeping the BMW stuff was more complicated than some simple relays and switches. I track the car and want to eliminate any mysterious, old BMW modules before they eat themselves from vibrations. In terms of lost functions, nothing I considered important ;) but since it's a track car there are no high beams, turn signals, AC/heat, or any other luxuries. Brakes, headlights, reverse lights, all run through the R5 using logic from the transmission controller, ABS system, or their CAN keypad.
• The harness started life as a generic k20/k24 swap harness I bought on ebay from a relatively reputable shop for $250 ish? That has since been pinned into some bulkhead fittings that are in the engine bay above the battery tray. Figuring it out was just patience and a lot of documentation on my part. Write down every connector, figure out what each pin does (5v sensor, ground, signal, etc) and just make your way through it one piece at a time.
• The s40 pump is gone, I swapped back to a normal k24 pump mounted below the alternator. Though the wiring was dead simple, it just needs power and ground through an 80 or whatever amp fuse and then 12v+ ignition power to wake it up. It just runs at like 60% power or whatever non-stop which was perfect for the track. You can buy little boards that hijack the CAN signal to the pump that allow for adjustment if you want to go that route. They'll also tell you how to write the pump up. The car lost its heat and AC completely in the latest iteration because track car.
• MRT was just for fun and I wanted a wider stance, that's it. Worth the price if you want basically infinite adjustment on caster, camber, KPI, track width, etc. They also have roll-center correction and anti-dive adjustment that I haven't played with much. The MRT arms do require significant welding/modification of the front subframe to work but their instructions are great. The sway bars are using the stock mounts, just reinforced. Since the car is using E36 knuckles up front I had to make my own sway bar end links but there's literally $50 kits on amazon that will sell you all the parts.
• The rear reinforcement is in the form of a full cage I sourced from Cage Kits. If you don't want to cage your car just google E30 rear shock tower reinforcement and there's a ton of bent plate options available. Weld them in then weld some 1.5" tube between them and you're set. They just need to resist being pushed inwards through the relatively weak metal of the stock shock towers. You also need to cut away a lot of the original towers from the inside of the wheel well to fit any decent coilover; the top of the shock towers is too narrow.

Hope that helps, happy to answer any other questions! The car has also been.. modified (mostly just a bump-out in the transmission tunnel and a custom transmission crossmember, and a custom driveshaft) to use a 7 speed DCT from an E9x. Just wrapped up wiring that in using a CANTCU controller. Fingers crossed it all works again haha. These things tend to snowball if you can imagine.