Hi airwethead,
Check out FMS home page and click "Forum" at
http://n.ethz.ch/student/mmoeller/fms/index_e.html
I built one of the parallel interface described under
Parallelport-PPM-Interface for my JR. With earlier versions
of FMS, the controls were jumpy as if there were lots of
noise coming from the line. But it works great with the newest
beta version of FMS. I'm on windows 98SE.
Good luck.