i have just got my 69 bird back on the road a week ago .it has been down 2 years ( oct ,08 ) . i do have one problem that was not there when i pulled the engine & transmission a couple of years ago. the turbo 400 floor shifter linkage needs adjusting it doe's not engage in park good ( want's to roll) unless it is pushed to park & not just selected to park. but my main question is - when pulling out on the highway while the car is building up speed to normal cruising speed. while the transmission is shifting up through the gears it make's a squall during shift's & it seam's that it is shifting late ( that it is shifting at higher speed's than it should) hitting third gear at 50 mph. before the transmission was removed it shifted smooth . ???

Make sure your modulator is connected to manifold vacuum source.

Another possible thing as well could be burnt tranny fluid.
Have you dropped the tranny oil and filter lately?

yes while the trans. was out i put new front & rear seal in , new filter & fluid.

Was the tranny ever rebuilt back when you pulled it? If so, was it stored for those 2 years dry (no fluid)?

If so, the seals may have dried up during storage.

Or, if it was never rebuilt, it might be time.

the tranny has never been rebuilt it has 61000 miles on it. it was not drained while stored , but some fluid did leak out of the tail shaft during removal. it still had fluid in it at the time i replaced the filter , when i droped the pan it had fluid in it.