Physicist trying to do engineering. Not going well. After advice with 4 axis gantry.

[JAZZCNC]

I was having a little play with the BoB today and with a meter I could see the voltages coming out of some of the pins (not quite 5V but 3.6V, which may either be normal or it's because I have had to use a PCI expansion slot in the PC as it didn't come with a parallel port).

Possibly because of the PCI. It's very common for modern PC's to only supply 3.6V. However this is BAD NEWS for CNC and you need close to 5v to work correctly.
With 3.6V you will have trouble because there isn't difference between HIGH and LOW.?
When I said 0v and 5V I actually should have also said LOW & HIGH because that what really matters to CNC. LOW is anything from 0v to 2.5v HIGH is anything thing from 3.1 to 5V.
So with only 3.6v there not enough difference between Hi - Low signals and just slight difference or drop in voltage can cause missed steps and all sorts of strange happenings.

Only letters could put after my name are "NFC" or "CFS" but Hope that helps expalin little more.