I got the OBD2 Reader to work after reading a posting on Renntech. I added the forum below if anyone else had this problem.
http://www.renntech.org/forums/index.php?/topic/9664-code-reader-equus-innova-3100c/
Now that the code reader is reading it had 0 codes.
We did have a broken wire on the Crankshaft Position Sensor (pinched,,, my fault) that happened when we took the engine out; We soldered the wire. I am replacing that sensor tomorrow morning just in case (at $230!!!!!). I doubt that is it because there's no reason soldering shouldn't have allowed for plenty of signal.
We have double and triple checked all wires. There are NO wires that aren't hooked up that either of us can find. Everything looks fine.