Ok, This is what "I" would do. Please note this is just what I would do in your situation. Others may do things differently.
First I would pull every plug from the bottom of the driver board except for J133 and 137 (lamp matrix)
From the driver board pull plugs J106 and 107 (solenoid and flasher power) Can't be too careful!
I would pull the power plug J502 off the sound board (who knows what sounds you would get with the CFBL sound chips and an Indy CPU in there)
At this point I would do a single lamp test through all the lamps with the existing CPU in to make sure it works and the faults are still there. If the faults disappear at this stage it may not be a CPU problem so maybe no need to go any further.
Take the Indy CPU complete and install it in the CFBL.
Connect all the ribbon cables on the CPU
Connect the power plug J210
Connect plug J205 direct switches (to get the menu buttons working)
Leave all other switch input plugs off.
Start her up. You will most likely get a lot of test report faults as nothing is connected. The lamp matrix should start working but may look unusual as it thinks its an Indy machine.
Do your lamp test and cross you fingers!! (Obviously the lamps names will be the Indy lamp names but you can use the lamp numbers to test)