A flashing O/D light is an indication that the transmission electronics are reporting an error.
There should be transmission error codes stored....I will be honest.....I do not know if they come up through the OBDII port.....or what is involved in reading them. When I had transmission issues....I had the diagnostics done for me at the dealer.
There are a number of wire harnesses around the transmission.....so I would check to make sure that all is plugged in....and that no wires got torn or pinched during the repair process.
The brake master cylinder is just over the transmission.....so verify that the wires to it are not pulled or damaged. There is a pressure switch on the bottom of the master cylinder....which is a high failure item. The main symptom is that the cruise control does not work. If the brake fluid is even very slightly low.....on my '96....both the Brake and ABS lights will come on.
The transmission range switch is on top of the transmission. The shift linkage connects to it....and it has a wire harness that connects to it.
The TRS is also a high failure item....double check the electrical connector.
I know that these sound like obvious items....
But...I would check these out before anything major. The wiring is very easy to damage...no matter how careful one is ....as it hangs down in the way....and has a tendancy to flop back down....right in your way while working... Also....we can hope that the solution is simple and easy....as well as cheap.
I am no expert on transmissions.
I did have mine replaced at about 100K miles.
The replacement unit is still going strong at 154K miles.
I did install an auxillary transmission cooler.
I have some pictures of a number of little repair projects on my '96 3.8L.
They may be of help to you for some of the other projects that come up in keeping a car in good shape....
http://community.webshots.com/album/201931518cScpNK