Mystery Solved!
My switch had gotten bumped and lost power. So my computer happily connected to my wifi and continued to work but had no access to the Access Point that my printer was on because that AP was Ethernet. So now that my computer is back on eithernet and wifi is off, all is well. Whew!

okay, I am back connected with Ethernet. Whew! I just needed to follow the "Fallback procedure #3" instructions exactly. hehe
Believe it or not, it DID fix my thermistor issue!
So I am up and running.

I think I figured it out for myself. I added these lines after the z endstop is triggered.

; Z Offset
G1 Y300 ; move back over bed
G1 Z0 ; move to 0
G92 Z.45 ; reset to actual height

Solved the prime line issue by editing the start gcode in Cura under machine settings. I am not sure why it had to be different between RRF and Marlin but it did.

@erice555 I am going to replace the X endstop and see if this is somehow a switch problem.

Thanks Phaedrux. I did indeed have the motor timeout set to 10. I changed it to 60 to solve another problem I was having and now I don't think I would have an issue here. The 17 second wait was for cooling on extremely small layers for PETG (where I have no fan on). The minimum layer time was 20.

I also took your advice on the Cura machine code and set m90 at the top.

Thanks again.

@t3p3tony https://www.amazon.com/gp/product/B088W8WMTB/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1

@erice555 Yep, that is exactly what happened. Remapped it to fan 8 (duex board) and all is well.

I was doing some wiring of my part fan (fan0) and I forgot to turn off the printer. I shorted the two wires together and the board rebooted. Now that I have it all rewired, the fan is on 100% all the time (even when not printing). Does that seem like how it would fail if I damaged my board?
If so, I assume it is possible to use a different fan port and somehow map that to my part fan?

@erice555 I seem to have this working. One can have a motor involved in more than one axis so I just have 4 extra axis a,b,c,d and adjust them as I need. Then I go straight into a print. It still homes Z and all just as it did, so I am golden. Thank you.

Edit: never mind the below. With some searching I figured out a G92 sets the homed state and then allows me to move the 'axis'. So far so good.

@phaedrux I made a good start on this but once I create my 4 independent axis, I don't have a way to home them. How can I fake them out that they are homed so I can move them?

@erice555 If P5 can only be part of one axis then I'll need to completely different config.g files. Will it switch config files without a restart?

@phaedrux Hmmm, seems rather involved but I think I can work it out. Will it let motors P5-P8 participate in more than one axis?
So like P5 can be part of Z and also U?

I have a core xy so there are 4 Z motors that move the gantry in the Z. My inductive probe is not triggering consistenly across the bed so I want to manually level the gantry by just using a piece of paper under the nozzle at each of the 4 corners of the bed. How do I move one Z motor independently of the others?

@gloomyandy Yes, that is what I was thinking of. I was running marlin and SKR 1.3 board. Does reprap have anything like that?

@jay_s_uk oh. I thought I remembered something from my Ender (which I no longer have) that there was a mode where the motors would monitor skipping and adjust/reduce their operating current accordingly. I guess that is a little different that what I said but it is what I was thinking about. Do you know what that is called?

Is there a way I can find out motor temperatures or get a log of motor temperatures over the course of a print?