Good news, everyone (I've been watching my complete Futurama collection all last week, so be prepared to hear that line more frequently :-P )
Anyway, I took the motherboard, Mediator and Apollo with me to work, hooked it up on a table and started working under a microscope on the old acid-leak from the battery I replaced the leaking original battery with. Seems there was some serious doodoo there. Anyway, I have only powered it on and heard the floppy click, but since this is excactly what DIDN'T work yesterday at home, I am willing to call it good news. Took me an hour to clean up the mess and do some reconnecting on the databus (between CPU and RAM). There was a LOT of damage around the 12V fan psu pins. Removed those completely.
Edit:
The _bad_ side to all of this is I really wanted to take out the drill and make a 1260. It might seem as if that's not gonna happen anytime soon. Would have been fun trying to order a 68060 as sample from Motorola :-D