Just to close the door on this one: it's fixed!

It was a little anti-climatic in the end even, it just worked. I wound up re-installing PathPilot and running all the updates, just to be safe (after backing up my offset library). I've now run a few conversational programs and regular Gcode and PathPilot is same as it ever was.

I do have an intermittent issue with the wireless dongle, it tends to make the computer hang a little and run slow, but I think this was an issue before I replaced the motherboard. Adding more than the stock 1 gig of ram (!!!) might help here, but that's on the back burner for now, at least I'm back to having a working machine. I don't love the dropbox method of transferring files anyway, it's too buggy and slow. I just use sneakernet to transfer files on a usb stick.

Thanks to everyone who commented in this thread, for anyone finding it in the distant future, the bottom line is that home-brewing your own PathPilot control with non-tormach hardware is quite do-able. Advisable, even, if you want to save a bit of $$$.