I doubt you have irreparably harmed RAMPS - it's pretty hard to do as it's simply an interface (unless you've done something terrible).
How did you jumper the VCC and 5V holes? soldered in a wire? you haven't bridged anything else by accident, have you? That'd be the first thing I check. Also, check the servo pins - make sure there are no bridges there.
Is D1 (under the X and Y stepper drivers) installed? I'm wondering where the power for the MEGA is coming from. Maybe your 5V regulator on the MEGA is damaged if it can't provide enough current for the 5V rail. By removing D1 the MEGA will pull 5V from the USB. Just heat one of D1's leads from underneath and add some solder to it, then (with the iron still on the leg and pad) use a pair of tweezers to gently pull the leg from the component side. Desoldering can suck. Just remember that excess solder is your friend here - you can always wick the excess out.
Oh, and get rid of those polyfuses. I'm not entirely sure why there are fuses on this board at all. I know,
SAFETY. But seriously, I
jumpered them out long ago. I simply live with the risk, which in my mind is minimal. I am much more concerned with a slipped thermistor on a hotend or heated bed. D:
And if you did blow your stack, I would not seriously consider any ARM based solutions unless you like living on the bleeding edge. Smoothie is great, but is nowhere near as complete as Marlin/Repetier. Either RAMBo or the X3 Pro, although the RAMBo is hard to beat for an all-in-one solution at that price point. And buy direct from Ultimachine - Johnny Russell @ Ultimachine designed it.

Then again...if you blow a driver you're kinda screwed. The X3 Pro solves that and then some - personally I like swapping pololus out when I blow one up for just $10.