OK. What you need first is commiseration from those who have also been there, done that, survived, and either triumphed or moved on. So, commiserations, then. Without being able, at this remove, to have any definitive opinion about the specific cause, I observe that what you describe fits the picture of a flakey MLB. You may never get a specific diagnosis, but the principle of test by replacement that you have employed in this affair is suggested for the main board also. If another board works ...

I was recently driven to the conclusion that the SCSI port (What? SCSI never fails!) of a IIci MLB had died, but not before quite a bit of argey-bargey. Best of fortune hereafter.

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