The wires were routed in a strange way, they were right down on the inside face of a frame bar near the transmission. They were evidently low enough to get cut, but far enough on the other side of said frame bar for me not to see that they were. These wires ran from the Lambda (O2) sensor to the Lambda module, that controls the mixture of the engine,. Two of the four wires were cut, so it was only getting half (if that) the information needed to make the engine run smoothly. I now know why the car was hesitating and not driving very well. I have now fixed the issue with crimp-on connectors (very nice :-P) and electrical tape. It looks good as new, well, just a little bigger than before :-).
Pictures of the cut wires, the connectors, taped up, and then finally done.
Must be time for a test drive :-D.