I see they do a free C Compiler too, so as and when I get the existing master software ported to C there would be an easy upgrade path (for me anyway). I don't know what the PBP serout/owout commands are doing, but most of the example C code I've found uses delay loops for timing which is an extremely inefficient use of the processor's time, so my first challenge is to get everything interrupt-driven. The nice thing about the Parallax is that you won't need to worry so much because you could easily run delay loops without affecting the other "cogs".
Not panicking yet, the wiring is in a bit of a mess and I haven't earthed the shielding on my data bus cables. Will have a look at it next week and see if I can track down the problem.