Considering your a doc,
I`ll give you some free advise. Your on the right diagnostic path. However your faced with task of Herculean proportions, and you seem to be slightly ill equipped (understandable since your not a full time BMW mechanic).
This project sounds fun, but if you look at it, you have two patients who both require extensive organ transplants, and you have no guarantee that the transplants will be accepted by the body, and allow it to maintain normal function levels.
1) Figure a way to access someone who has the access to the BMW system diagnostic software. Im pretty sure, if you try to purchase access, your looking at alot of money.
2) Your water level damage is quite significant, and since the electronics are usually located near the floor of the vehicle your looking at a alot of money to either replace, recode, or even diagnose the issues at hand. If your warranty, which doesn't apply anymore, was available, the dealer would simply order every single module, wiring harness, and connector. Their estimate would be significant.
I don`t want to come off as harsh, but I wanted to assist you in determining whether this project is a financial gain or loss. In medicine, the H oath you take, is to always care for your patient. However sometimes you come to a point, where it simply isn`t humanly and as satisfactory diagnostician possible to do that. This is one of those times.
Finally, I STRONGLY WANT TO SAY, My words, opinion, suggestions, and anything I have said, is my opinion.
Its is always your choice to ignore, or take my advise. For all you know, I maybe
a) Cautionary idiot
b) Realistic Well-wisher
WHO KNOWSS....G luck!
BTW maruti 800, HM ambassdor, maruti omni, any indian car (MM, Tata) are soo easy to work with. Their powertrains are archaic, but simple and solid.
BMW and Mercedes Build Beta Products!
Lexus build Release Candidate Products!
Why does this matter?
CAUSE EVERY TIME someone says Lexus has better build quality, one should consider what Toyota their Lexus Engine and chassis platform comes out of and how long that part has been tested in the real world!