Ok, here's the run down.

I have a 96 GT Stang, NA all around. I have a front U-Joint blow out on me and take out my transmission. I got a new trans out of an '02 Crown Vic Interceptor. I know the pin out is different and I got a pigtail from Ford to plug into it. I got the schematic to change it over to the 96 wiring from this site:
http://www.p71interceptor.com/tranny/diagrams/electrical/external/bulkhead/index.html

I made sure things were good and tight. I did though, have the wiring incorrect, and it threw error codes that I read with the OBDII scanner to find out that I had them wrong. After getting the wiring correct, I was still having problems with shifting.

I have 1st, 3rd, and what appears to be O/D, but isn't.
I do not have Reverse or 2nd gear.

When I start off in D, if I get it up to 21mph, it'll shift into 3rd when I let off the gas a little. If I don't get to 21mph, and let off the gas, rpm's drop. When I put the peddle back down, it'll rev up and hit like I have a clutch, instead of an automatic.

Once it shifts into 3rd, and I accelerate gradually, and leave the O/D turned on, it'll drop out of gear around 40mph, re-engage around 25mph. If I turn off O/D, it'll stay in gear and I can drive "normally".
If I put it into manual 1st, I have a normal 1st gear, where when you accelerate, and let off the gas, it'll rpm decelerate. If I put it into manual 2nd, it'll do the same thing as in D, but won't shift into 3rd, or 2nd.

Thing is, if I have the rear end off the ground, and drop it into reverse, the rear wheels will start to turn, slowly, can be stopped by hand. If it's on the ground, no motion what so ever, even under rev'ing conditions. When shifted into R from P, there'll be a clunk.

This transmission was rebuilt by a guy in Georgia with all OEM parts. Here's the list he gave me that he did:
new direct clutches- increased from 6 to 7 clutches (+1 steel plate)
new forward clutches - increased from 5 to 6 clutches (+1 steel plate)
new intermediate clutches.
updated mechanical diode one way clutch (reverse drum
new O/D band
new front pump seal
new front pump o-ring  
new extension housing gasket
new out put shaft seal
new valve body gaskets.
new filter and pan gasket.

One guy from TCCOA.com forums stated that it might be a seal in the 2nd/Reverse clutch assembly that needs to be replaced because of possible damage. The guy that rebuilt it, said he'd take a look at it, but I have to take it up there to find out if that's the problem. I'd hate to have to 800 miles to find out that it was something I could fix here.

If there's anything anyone can help me out with this one, it'd be greatly appreciated.

Thanks,
BH  

forgot to mention that recently, the O/D light has started flashing at me. It doesn't stop flashing in "code" form. Just when I either slow down and it drops out of 3rd, or I guess it gets tired of flashing. I counted one time, and it went up into the 40's before it stopped. I don't know the exact number, tho.
And, I've tried pulling codes off using the OBDII scanner, no luck.

Also, adding to the when I have the O/D turned off, it'll go into 3rd, after a few moments of cruise speed, the rpms drop slightly (tc locking?)  

No one has any ideas?  

So theres all these views, but no one has any input on the problem.    

get used to no replies here. if you post a question that the masses cant answer you get total silence. and by that last statement i mean a simple fuel, air, spark problem that everybody and their mother has had they will ignore you and hope you go away. i love the mag but these forums have the "i bought it this way" crowd. you know the guys right? the kind that cant, and i do mean cant, change their own plugs, have no idea where to hook up a fuel pressure gauge, or past jumping the battery have no clue what to do when their cars wont start. i would think such a fine publication would have a little better forum than this but apparentley i was mistaken. i think i'll take my happy ass to stangnet see if they can help hope that didnt help
later ***
  andy9802gt