89 735iL Transmission problem

i have a 1989 e32 735il, I recently had tranny out to check seal. all the fluid was drained out the car has not been run for at least 5 years i recently bought it from my buddy. I put the tranny back in and put 3.5 quarts of fluid in and its still not up to the full mark. also the tranny does not want to come out of first gear, the shifter will move it to each gear but it will not shift outta first. any help or ideas would be great. I do have the car on jack stands running it, not sure if that matters.

Thanks
Feit87