I’m sorry to hear you’re still in trouble with these.
Well, I’m looking at your picture, and here’s what I would do, just for trying (in that order) :
– put the CXA back (I understand you’ve already did that).
– connecting the mini mega to different +5 and grd points ( a capacitor would be fine).
– disconnect the switchless board and try without it, just to see.
– check for false contacts on the VDP, could be a little solder which leaked to a pin beside another one.
– with all these mods, you can try to use a power brick with 9V and at least 2A (I use one with 2,5A).
– recapping the system with new capacitors + new voltage regulators (last thing to do because it’s quite long).
Honestly, I would find it very strange that an rgb bypass amp kills an entire system, because it’s just dealing with video and nothing else. But I know that the more you add mods on a megadrive, the more you expose yourself to risks of interferences between them, and sometimes it could be a tiny thing to change to get everything sorted out. But I understand it could be a pain in the back sometimes.
Please let us know about you’re investigations.