Hi,
I didn't have much time these last three days, but I've been following your problems... Seems like your mega took a lot, I'm surprised it still partially works. FIY, You can find mega2560 clones on
dx.com for 20$, might be worth the try if it happens again (since you already ordered one).
RAMPS is mostly passive components and headers, except for the three big mosfets, so until the pcb is damaged, I think you can keep yours.
(If you don't have any spare, I recommend sourcing some extra Pololu drivers just_in_case. It's really frustrating to wait only for these little pcbs...)
Be careful when switching mosfets, I'm not sure D9 can handle the load of the Heatbed... Might be a good idea to check before trying. The heatbed of the Sc is a standard Mk1 heatbed (should be written on the top of the bed), resistance should be around 1 ohm (
http://www.thingiverse.com/thing:3919) so I think the MOSFET can handle it. On my RAMPS (1.3) I don't have any heatsink and the MOSFET works fine, even for (quite) a long time.
I don't see any reason you couldn't find a replacement for T0 and T1 to keep your changes just be careful when you update your firmware. I'd say, leave the RAMPS board untouched, so you can return to normal when your arduino arrives.
If the first layer doesn't stick enough to the cold heatbed, try with kapton taped, and clean it with a little bit of alcohol just before the print, it might help a little bit...
Good job on your debug, it doesn't look really easy.