The problem with the Y axis limit is solved... I noticed that one of the Omron limit switches was broken and had been jerry rigged with some wire around the threads. It was a creative fix, but I located three new switches for $25 so I figured I'd fix it. Anyhow, while in there, it occurred to me that whoever wrapped that switch may have screwed up the order. So I did a quick check.... Sure enough, the max and min were reversed. Both functioned as limit stops, but the ability to back off the limit was working against the operator. You could only advance *further* into the over travel instead of correcting it. So, I swapped the two limit switches (the third is for the origin reference operation) and Voila! Everything works again.