Transmission rebuild

I didn't want to tackle it, but with business how it is, I reluctantly agreed, (I under quoted it!) And I got bit by the E Drum, no fifth and sixth gear. I put new seals in it, and the drum holds perfect when air checked. When I assemble the entire gear train, I see that it also pressurizes the shaft going all the way to the back of the transmission and it doesn't air check. I installed a omega machine bushing kit in it ($122.00). What advice does anyone have to make this run right?