Ok, final update: It now works. I gave a few good pushes on the MiniMegi board and I think that may have completely seated it. I think I may have slightly deformed the motherboard socket pins and the MiniMegi may not be sitting in there as snug as it should be. I think it may actually be "floating in the socket" if you know what I mean. I am going to open it up and re-straighten or re-align the pins on the motherboard to grab the chip better. Thanks for everybodies help.
I have one small question. Out of curiosity, what would happen if sombody were to remove their regular agnus from their A2000 and install the Agnus from the A3000? Would that work, or would it crash the machine? Thanks.