I found the solution and fixed mine, by disconnecting the power to the automatic antenna. Now, the courtesy light switch in the door functions properly, lights go on and off as they should. I'd love to know how the wiring between the courtesy lights and the antenna relate. There is a power strip in the driver's footwell, but I have not investigated further.

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87 300e (white/black; amg body kit)
88 300ce (red/cream; amg body kit)
93 300ce cabrio (white/blue/blue top)
93 300ce cabrio (black/grey/black top)
98 ml 320 (totaled @ 137,000 miles)
99 clk320 (black/grey/black top)

I believe I found the problem with the courtesy lights.
1. I pushed the reflector in and it popped out. After inspecting the part I removed a burnt out bulb. I ordered the bulb from Pelican and expect it soon.
Will post results and commentary as necessary.

Courtesy light- bad switch- waiting for replacement
Main wiring harness is not bad- the starter alternator harness has broken insulation p/n 1245403130
Beautiful car --I cringe at the thought of a $3000 part going bad
No one has been able to give me a fix for the flickering lights