Well I removed the old chip and put on the new one, but somethings wrong, the chip showed up on my computer, when I first plugged in my Arduino to program the new chip, as a atmega16u2 DFU mode, so I powered up FLIP and burned the firmware through the USB port (one of the things wrong is that I can't program the chip through the ICSP header, it doesn't respond with anything, it appears that it sees the chip as being there, partially (hard to explain at the moment cause its hard to remember and its been several days since I had tried to program it, college was keeping me busy), anyways I do have issues trying to burn the bootloader back onto the mega2560, I think its issues from how I modified my Parallel programmer, I had resoldered all the wires so as to shorten the 2 foot 8 inch cable to a 2 foot 7 inch cable and soldered the exposed wire in the cord (which comes in contact with the "Faraday" shield) to try and help block interference, though the length of the cord is probably too long, but I digress, when I try to burn the bootloader back onto the mega2560, most of the attempts end with a supposedly successful writing, but 2 of the fuses are changed in the process, and I am still unable to communicate serially with my Arduino or even program it.
any insight on the length of my parallel cables?
what about theories of what may be wrong on my Arduino that is still preventing serial communication? it doesn't appear to have any shorts (visible at least), and the only two contacts that I lifted from the board by accident when applying new solder for the 16u2 where for unconnected pins on the chip and are therefore unneeded.
also as a side note, it seams that my Arduino is now partially powered when I plug my parallel programmer into the iscp headers (it happens with both); I don't recall it doing this before the work and therefore leads me to believe that there is a short somewhere.
again thanks in advance for any help, comments, insight, or anything