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Hmm, I must have made a mistake when measuring the signals. The Tang gives out a perfect 50% duty cycle. I was sure that the level shifter made the same. however they did not. The level shifters make something weird out of it. The level shifter have EL817 coupler on them. The datasheet shows cut off frequency fc =80khz. If I read that right I should not even be around 25% of what they should be able to do. They do have an LED, I wonder if a pulldown resistor would help???

I think @meister said, that I could connected the breakout board directly to the outputs of the Tang. I might try that.

 
 

OK that's probably supported.

When I get a chance I can make firmware for a 7I76E with one Fanuc
channel on the serial expansion port for testing. I seems that that's a 1M
CPR encoder.

Yes, it’s 4 wire - here’s a section of the schematic that labels the wires: 

 

Labels read: SPD, *SPD, SPQR, *SPQR. 

Earlier today I plugged those four wires on the live tool motor into the encoder input on the ultra3000 drive with 4.7k pull-ups to 5v thinking it was an incremental pulse coder… I’m hoping that didn’t cause damage 

Won't last, it's a tool table index issue. It will start again randomly. Be careful since you're using atc as it may or may not cause an issue.

just as an aside, I uninstalled and reinstalled using the deb method with no issues whatsoever. Took about 15 minutes total to download and do everything. At the least I might try a second SSD and have a 2.9.3 version ready to go just in case, cheap insurance if you're using for business. Also, it may be wise to remain on the lockdown version until they release 2.10 as lockdown. Will avoid these hiccups in future.

Hostmot2 has support for the older RS-422 (4 wire = req/data) Fanuc pulsecoders
Can you find the pinout of your encoders?