1990 Sr5 Shifting Issue

I recently had a tranny put in it has around 30grand on it and it also has a new clutch. I ajusted the pedal and still it seems to be hard to shift in to first/reverse and i dont see what else it could be.I cannot find any leaks in the master or slave cylinder, any ideas or things to try would be very appreciated.

Pyro

Air in the hydraulic system.
Worn pivot points.
Deteriorated flex line.
Worn push rods.