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Well, reading this and the rest of this thread, I can't think of anything else. Since you ruled out pretty much everything else, I would now put my money on one of the parts shorted during cleaning.. anecdotally I've heard parts dying by shorting them with your fingers, but it never happened to me, so that would be pretty unlucky.
Last time I did a cleaning of a particularly dusty system, a dustbunny flew in the PCI-e port without us noticing (it was dark and circumstances were not ideal). With the GPU Re-inserted, that was enough for the system to behave similarly to yours, but you re-seated everything so... That would eliminate this as a possibility.
You could share a photo of the current situation, a top down of the mobo? Eliminate chances you are missing something by secondary means(as opposed to just text)?