Ok, to give a bit more detail:
The 100 ohm resistor R1 is required for the PGM to recognise the cartridge. All original cartridges that I opened up seem to have it, when I put together the first prog PCB it didn't work until I added the 100 Ohm resistor.
R2-R4 can be used as pull-up resistors (10k) for the GAL inputs. The GAL should have built-in pull up resistors, but some people had problems getting cartridges to work without them. There is also a version of the GAL with pin-keeper circuits, which will just hold the previous input, but not pull it up.
You could also hard-code your preferred options in the GAL sourcecode, then you don't need to worry about the pull up resistors at all.