Ruiner46 wrote:Update:
Signs of life!  I made a cable and loaded the bootloader back onto the Atmega using ponyprog.  Now it powers up to the bootloader.  When I push down and it displays "Send Sysex now", the MIDI light comes on right away.  However, when I try and send sysex firmware using MIDI-Ox, MIDI-Ox will hang forever and apparently not send.  The MIDI LED never turns off or flickers after I push down on megadrum.
I also tried using MCT, but I get an error everytime I try to update the firmware. 
Any ideas?
The ideas:
1. Not correct MIDI ports selected in MIDI-OX or MCT
2. Incorrect frequency selected in the bootloader.
3. Broken connectivity or shorts between Atmega (pins 14/15) and PIC18F2550 (pins 17/18)
4. Something broken with drivers installtion in Windows.
5. Partially broken Atmega or/and PIC18F2550
Since you can directly program Atmega, program it with MegaDrum firmware via ISP using ponyprog (.hex file, not .syx file!). Once programmed test MIDI communication using MIDI-OX or MCT. Do you get two way MIDI communication with MegaDrum firmware?