Meowmiev, welcome to the forum, thank you for your kind words and for your very precise description of the problem you've experienced. Delighted that you still like your i-MiEV (as all of us on this forum do), despite it's annoying issue.
I'm pleasantly surprised that the car is fully operable without any visible error indicators with the air conditioning compressor disconnected. This in itself is strange (but welcome in this case), as this car has so many interlocks which result in throwing a code if they're disturbed.
If I recall, that compressor is powered directly by the car's high voltage battery.
I'd like to try to get the ball rolling in helping you -
1) Is there a possibility that water damage might be covered by one's car insurance? If you have full coverage, it might be worth a call to the insurance company to tell them that this is what happened and would they please pay for it (after the deductible). Certainly worth a try.
2) There is a history of AC compressor mounting bracket failures, which have subsequently resulted in compressor issues and wiring damage. Presumably the dealer inspected this, but it may well be worth having a detailed physical look at this assembly including the wiring leading up to it. After disconnection, I would hope that the dealer adequately sealed the ends of the (disconnected) connectors to protect them from the elements. I don't have the wiring diagrams with me, but maybe someone can comment as I suspect the (very dangerous) high voltage wiring to the AC was probably left undisturbed.
3) Anyone have any ideas on how to troubleshoot the air compressor that is allegedly "shorted"?
4) Next, let's assume that the compressor itself is defective - inasmuch as your dealer wants over $4000
to replace this unit with a new one, perhaps we need to find you a used one? I wasn't able to find anything after a brief search on eBay, but, before searching the massive used car parts networks, does anyone have access to a parts car?
I just visited with Ben Nelson in Minnesota yesterday (before I read this post) so will give him a call as to his thoughts about the state of that compressor on the hurricane Sandy salvage i-MiEV he just parted with (not too hopeful).
Welcome ideas anyone might have to help fix this problem, as next summer's life in New Orleans without AC is not pleasant to contemplate.