I have just replaced the trans and everything went well but it will not shift. Reverse and drive both have plenty of pull but it will not change gears. Fluid is fresh and everything else looks ok. Anyone have any ideas?

Fluid is fresh.... but is it full??

Sure is ran it for over an hour and rechecked it every 10 minutes.

Does it go into Drive and Reverse and is the neutral positon of the shifter all right? First off I would check the shift cable. It may need adjustment.
I'm not too well versed on the 88's but there may be a vacuum line going to the modulator that isn't hooked up. That, and check for dirty or loose wiring harnesses if it has electrical shift solenoids.