You could get a serial mouse drivers from Aminet and 9-25pin adapter to get the PC mouse working. You can use it temporarily till you find real problem. Make sure you have a cheap serial mouse, I have Logitec one and the drivers are not very compatible. I have a mouse with PC/MS switch, the mouse works fine in one of those settings, forgot which one.
But, there is a big drawback, this can only be used in Workbench environment. Games, software booted from floppies would not work.
I have a spare A3000 with bad mouse port and that's what I'm using for now till I get a chance to fix it or sell it for parts.