I don't know if this is related...sounds like it might be...I found a link over at e46forums about Bremi packs failing due to internal insulation failure. Mine are all Bremi, makes me worry a bit. The odd thing is that the BMW TSB recommended changing all of them...not one at a time, like when the Bosch coils fail.
I know you tested with another set of coils, but I'd probably try the original external coils & wires if you still have them. I have three known good coils from an e30...if you need them for testing I'll send 'em along for postage. $5 gets you a flat rate box...send them back when you've fixed it. I wish I had all four, but I sent one along with my spare DME to another member who had similar problems.
Here it is, along with a few others:
Bad DME & coil thread
Bad motor wiring harness thread
Bad #3 wire thread
There is a date stamped on the coil for production week/year. The effected Bremi coils are
42/2002 or earlier, or in the range from 01/03 up to 24/03. Mine are all older than 2002, so I'll be on the lookout for this too. Likely they were pulled from an M70; nobody who owns a newer BMW will touch the Bremi coils so they're cheap. IIRC, the early Bosch units were also pretty bad, the Bremi's were supposed to fix the trouble.
It doesn't fit your symptoms exactly, but it's close. Any chance you'd take those coil packs to a dealer to have them tested? Know anyone with a GT1? If you were closer I'd hook you up with my BMW mech buddy...I try to avoid dealers as much as possible, but there's a place & time for everything. Not that many BMW dealers will touch anything older than 2000, but it might be worth your time. I hear your frustration, I hate when I can't get a car or bike running right. But trust me, once you get this car running right you'll be glad you did.
http://forum.e46fanatics.com/showthread.php?t=226581SITUATION
Engine may run rough and "Check Engine" light is illuminated. Misfire faults are stored in DME control module.
CAUSE
Reduced ignition firing power of BREMI coils due to coil internal insulation deterioration.
CORRECTION
Follow the appropriate Test Plan from DIS Plus/GT1.
If BREMI ignition coil is found to be defective, and the production date stamped on top of other coils housing's is
42/2002 or earlier, or in the range from 01/03 up to 24/03 all six coils must be replaced . For replacement instructions
refer to RA 12 13 511 found in BMW TIS.
Only coils manufactured by BREMI are affected. BREMI coils are easily recognizable by the all black, shiny housings.
Bosch coils, which can also be fitted in M roadster/coupe and M3 vehicles with S54 engines, are not affected and should
NOT be replaced as a set. Bosch coils have a silver, aluminum housing.