I'm working on answering my own questions via more forum searches/reading.
To program the PIC for USB.
1. Connect USB cable to USB port on MegaDrum (which requires me to connect USB from Jacks board to main board)
2. On same computer connect DB9/ISCP cable on MegaDrum
3. Use
WinPic.4. Options tab->Programmer options check the first 6 boxes
5. choose "JDM (2) for serial port" in the "Interface" tab
6. select PIC18F2550 in the "Device Config" tab.
7. open the hex file with the MIDI firmware and then select "Device->Program (CODE+DATA+CONFIG)" in the menu.
If programming succeeds you'll see "Programming finished. no errors" at the bottom in the status bar.