Just an update:
My body decided that last week would be a great time to acquire an infection, so I've been too sick to try messing with my Arduino until today, so I decided to give the re-flash a try.
Unfortunately, I've hit a snag. All the posts in the thread posted earlier (this: http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1286088093/30#34) point to another forum post for visual directions on how to put the Arduino into DFU mode to update the firmware.. this link, specifically: http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1285962838/10#10
However, whenever I try to open that link for further direction, I just get an error: Error: You are not allowed to access this section.
Is there an alternate location for this information? I've tried searching the net, but every other piece of info I've found on putting the Arduino in DFU mode just links back to that same inaccessible forum post. I also found some info in the README on the Arduino firmware github page: https://github.com/arduino/Arduino/tree/master/hardware/arduino/firmwares/arduino-usbserial/ but it simply says:
4.a. assert and hold the 8U2's RESET line
4.b. assert and hold the 8U2's HWB line
4.c. release the 8U2's RESET line
4.d. release the 8U2's HWB line
I can figure out the reset part just fine, but as for HWB, I'm not as confident. I tried tracing lines from looking at the Mega's schematic: http://arduino.cc/en/uploads/Main/arduino-mega2560-schematic.pdf but I'm still not sure if I'm looking at it right, and I don't wanna accidentally fry my board....
Any further suggestions? thanks!
EDIT:
I just got it working. I found a supposed reproduction of the original image from the error-ing post i mentioned earlier here: Arduino UNO | PDF | Arduino | Computing
and, following some tips from the original thread in this reply: http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1286088093/45#56 on how to modify the instructions for the 2560, i was successfully able to re-flash the firmware, and the IDE now works correctly. I was able to upload new sketches immediately, and all appears to be well. Thank you very much stimmer for posting the link to the thread, and thank you wombat42 and baum for your insights!
One final note to anybody stumbling across this in the future: my only fumbling point was that I was not immediately able to determine which capacitor to short to on the 2560 (since the guide was designed with the Uno in mind). To figure it out, just read comment 56 that I linked to immediately above, and keep the 2560 aligned in the same way as the Uno is on the scribd image (i.e. USB port to the left), and it should be obvious. hope that helps!