Its been a few days but I finally got a chance to go look at the truck again. I hooked it up to my scanner and pulled 12 codes. Here they are:
P0301-cylinder 1 misfire (no biggy, I'll check on this once I get evreything else sorted out)
P1747-Electronic press control solenoid short circuit
P0750-Shift solenoid A malfunction
P0755-Shift solenoid B malfunction
P0743-Torque converter clutch circuit electrical
P0443-EVAP emission control system purge control valve circuit malfunction
P1451-EVAP control system vent control valve circuit malfunction
P0135-O2 B1S1 heater circuit malfunction
P0141-O2 B1S2 heater circuit malfunction
P0155-O2 B2S1 heater circuit malfunction
P0161-O2 B2S2 heater circuit malfunction
P1409-EGR EVR control circuit fault

I also found out the the trans supposedly worked when it was swapped but then the engine started running badly and the trans quit at the same time. I called around to see what a replacement tranny would cost and found out that there were two different ones install and they are not interchangable. The one that came out had the number
YL3Z 7000 FA on it. The one in the truck now has the numbers YL3Z 7000 LA. Does this anything to be worried about?
Another thing I noticed while I was looking at the tag was the mysterious O2 plug that was missing is clamped between the block and bellhousing. Can this be the whole problem?
Maybe all this info will help.

I quoted a post out of another thread that I have posted. I need some serious help. If you look in the 97-03 thread under the same title you will see the whole thread. PLEASE HELP!!!!!<!-- controls -->

 

Fix the wire issue with the o2 sensors and check fuse #23. Clear codes and recheck.

Edit- Sorry I just read your other post, good luck.

 

Yes, that could be the entire problem.

 

Well I've cut the wires to the o2 sensor to get the short fixed. I have another connector to fix the the one I cut off but I just haven't put it on yet. The transmission worked for about 100 yards then quit again. I'm wondering if the wires on the sensor could be shorting out still. I'm gonna try to replace this either tonight or tomorrow. I also think that I checked the wrong fuse under the dash. I checked #29. I think I should have checked #20.

 

Ok I went and replaced the o2 sensor harness and now I don't have the 02 codes anymore. One problem down, one to go. I went to fordparts.com and searched for the transmission assembly that goes into the truck per the vin number. The one in the truck, like I said is yl3z-la. The one according to ford is supposed to be yl3P-**. This is possibly the whole problem. So if that is the problem is there anything I can do to keep from having to buy another transmission? Say change out the solenoids for the ones that would go into the yl3p trans versus the yl3z? Any thoughts?

 

I just got off the phone with the local ford dealer talking to the service manager. He and I are good buddies. He told me that to engage gear is totally hydraulic. The electronics only controls the shifting. He said I need to check the valve body for a sticking valve. That makes more sense after really thinking about what the transmission is and is not doing.

 

Well I got it fixed. I don't know if it was the valve body, the filter, or the trans fluid that did it but it works. Thanks for all the advice and if I can help anyone else just let me know.