Make sure that the box under the seat does not have ANY corrosion left in it. Check all of the connections to the box to make sure that the wires and connections on the plugs don't have any corrosion.
I have a water damaged car that I repaired and I had to replace the immobilizer box, and one of the plugs. It had sat wet for a long time though.
If you replace the immobilizer box with a used one (check eBay), you need the immobilizer box + DME box (from the trunk), + a matching transponder all from the same car (that is the same model and year range as yours).
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