Incidently, the spindle will sync quite well for short thread lengths, but from what I have heard is that after a few inches of length for threads the timing gets muddled or something. I believe it's something like four inches or so. I've threaded several items without problems... one was the ballscrew end for bearing block mounting of my router after cutting it to length. I hope you can live with your limited use of Mach3turn until the super low cost of Mach4 comes out.
Nice work, BTW.
My understanding is that Mach3 uses one sync pulse on the spindle, and an averaging algorithm to determine z movement speed.
This is fine if your spindle speed is absolutely rock solid, but if it wavers slightly (say, when cutting metal) ;-) then the rotational accuracy/z position suffers.
For my LinuxCNC build, I'm following the usual way for LinuxCNC - an index pulse, and a number of sub-pulses (32? 64??) to actually give pretty good rotational accuracy.
Really, if you think about it, the averaging speed scheme can only result in inaccuracy, unless you have a rock-solid spindle drive. I don't know about you, but none of my lathes (4) are rock-solid; my 11x24 one is pretty good, but the clutch needs re-adjustment.
I'm not sure how many sub-pulses to give my lathe spindle - something to experiment with when I get it running.
I'm very happy with LinuxCNC and my mill hardware, I expect the same level of gratification with my lathe build - but time will tell...