I bought the replacement circuitboard ICM280 for my Goodman GMPN 060 furnace. The instructions only address the wires that are included in the upgraded wiring harness. 1. Do I replace all wires removed from the original board? The replacement wiring kit replaces all the thermostat wires, but the white wire goes through a multi-wire connecting plug on the combustion compartment floor, through a limit switch on the ID Fan. 2. Do I replace the existing white thermo wire by removing the multi-wire plug and installing the stripped end into the plug, or should I bypass this connecting plug and wire-nut the wires making up the circuit to the switch?

You follow the directions that came with the new board exactly.

http://www.icmcontrols.com/downloads/ICM280-ig.pdf

If you do not feel comfortable doing the wiring I suggest you hire a professional. They get paid the big bucks because they know how to read and follow a install sheet and wire exactly how the sheet says.