In typical form I solve the problem once I post. I managed to find the antenna amplifier in the C pillar. Once I took the trim off, I tried the radio and of course it started working perfectly. I eventually found it was merely a loose connection on the amplifier.

Since coming in from 35 odd C weather fixing it, I also just found a service bulletin in the BMW TIS referring to the E46 stating the coax connector from the antennad amp to the head unit can come loose. Obviously it applies to E36 also since that's exactly what had happened to mine.

I'm happy as I can now listen to my cricket and I assume I'll get better FM (i.e. better RDS - not that much exists)

The alternator whine is still just there, but I don't think I'll bother fixing that since it's pretty quiet and I don't listen to the radio that much. See how it goes.