Wiring Bug... or Software Bug

[MSURunner]

Okay, I've apparently got a bug somewhere... I was running into issues when I first switched to .83 Repetier where it was assuming my printer was 10x's taller than it actually was. That seemed to magically and mysteriously disappear later. Then I was running into issues where the printer was stalling out transitioning between layer 1 and 2 (always and always in the same spot), in addition to (not that it was a particularly big deal) stalling whenever there was a prompt for a retraction in the firmware using the OPS (I know, just use the slicer's retraction and call it good, but for diagnostic purposes it's out there). I tried reflashing the firmware, no change. I tried .91 Repetier as it's out there now, went through (rather exhaustively) rearranging a lot of the configuration.h file to better match what we are used to seeing from the older versions and ensuring everything is correct. Now when I go to print something, it attempts to move dramatically to the negative y and assumes a height of 505 mm (which I have absolutely NO idea where it's getting that height).

So here's the dilemma. I've modified the harness a bit from initial build by moving the extruder to the top plate and swapping hotends. The printer has also traveled several hundred miles in the back of my SUV to go present FDM printing at our State Educator's Conference. So while I had been getting good results and I am fairly sure I don't have any wiring issues, I can't be certain. I just placed the order for an Onyx now that they are back in stock and so I'm going to have some re-wiring to do anyways. I could probably benefit from a bit better routing and taking some of the initial stepper/heater wire and replacing it with shielded, but I'm not 100% sold that interference is to blame on any of this. What do you guys think? Is this sounding like a wiring issue, a hardware issue, or some sort of software glitch? I would really like to be able to use it this week since I was planning on doing some upgrades on the UM and the students have projects that need printing, so while I'm about to tear it completely down and rebuild it (soooooo not looking forward to it, but I know I'll better assemble it now that I have already tore through everything and know where it's going), I'd like to be able to postpone that for a week or two if at all possible.

[Polygonhell]

Well I'd start with a known correctly configured firmware, to eliminate that, and then move onto the simple stuff, does it home, can you get through configuration etc.

[Jimustanguitar]

I'd also try printing a known good file (One that you sliced before any changes and that you know creates a good part). Have you looked at the code for the spot where this is happening?

[MSURunner]

Well, unfortunately I can't really start from a "known" firmware as the laptop that had my previous versions lost it's hard drive. I did start with the .83 that I emailed my co-worker and is working correctly on his nearly identical machine and sliced models that have printed well in the past/well on his machine. The machine does home correctly and displays the correct values as far as z height and printer radius in both of the configurations of firmware I've tried, it's just having issues when it comes to printing. .83 is still freezing, .91 is going wherever it pleases on the first setup.... just for the sake of examining firmware, I've included both versions. If you think there might be an issue with that I'm all ears. Now there are a couple of small differences in how we have wired our setups and he is a Rev1 Rambo, I have an updated Rambo. Having said that, we have made the firmware changes that would correspond with the 16th stepping and movement is correct in the .83 as far as distances go. It just stalls out. The .91 goes so haywire, I can't confirm much of anything. As such, I'm inclined to believe it is a hardware/wiring issue... Thoughts?

[MSURunner]

I just confirmed today as well that the .83 is working after the stall out on the initial layer switch to the second. At first I thought it might be interference related with sending power to the part cooling fans, but during a no cooling print (sliced with KS), it did the same stall. It was a small print so it completed without another stall, but I've noticed stalls on larger prints later as well.

[Polygonhell]

Ok so when you say stall, what exactly happens?
Does the machine just stop, or something else?