Was it an 040 at 40Mhz?
These get really hot and the Apollo 1240 card has the puniest cooling I ever saw. The original PSUs for the 1200 deliver about 30W before they cook. A hard disk, 040 accelerator and 16Mb add a motor and a few tens of millions extra transistors to your system, all of which suck juice from the supply.
060's draw much less power (static 3.3v design).
It really does sound like you have cooked your PSU.
Have you been able to test the bare machine (no accelerator / HD) on another PSU? It's probably not the main board thats damaged (unless you can see that it is, of course).
Its also possible that only your PSU is damaged, everything else may be ok.
If you can demonstrate that your maiboard is OK, hunt for a beefier PSU or convert a PC one.
Before I moved to a tower, I had a 200W PSU connected to my desktop A1200 for some time. I had two power rails into the thing - the original connector, plus an additional one I fitted into the case that fed the drives and supplied additional power to the mzinboard via the floppy power connector. I even got a 3.5 inch case cooling fan into the thing into the top left of the case, over the TV modulator assembly ;-)
-edit-
if your mainboard still doesn't work, it may only be the voltage regulators that are damaged - ie you might be able to replace them...
