Why Fight it?

The Fadal is a TRM mill.
It has color LCD monitor and from what I understand the latest version of there control before the were no longer made.
It has a 8gig memory expansion card as well.
The deal with a pro type control is everything you touch for it is high as h*ll. Just to add a fourth axes is stupid money. I don't want to be shackled to a couple of part vendors that are licking there chops every time I need to upgrade or fix the control.
My plan is to get PathPilot up and going test it on my Tormach to ensure it works properly and get it setup running Clear Path motors. I'm going to fix the Fadal contol and part it out to offset the cost of this build.

The ridge tap mean nothing to me. I tap with a floating taping and I do just fine.

the spindle encoder goes directly to the mesa board. the BOB doesnt' interpret it. just passes it thru so there should no concern here.

smgvbest, are you talking about a 7i76 board? If I understand the OP correctly, he is not planning to use one. He plans to connect a 5i25/6i25 directly to the Tormach Control Board which will out put Step/Direction and has other I/O for limit switches and VFD Spindle Control (but not encoder input).

Yes, my bad. my head is on the lathe more than the mill and I was thinking lathe.
But as mentioned by andy, one could use the other port on the mesa and a BOB to add the encoder.