it could just be that the gear selector rods haven't been aligned properly.
if the splines on the rod that come throught the bulk head in to the engine bay are just one spline out one way you wont hit 5th but if it one spline the other way you wont hit reverse.
as for the knocking check that the driveshaft bolts are tightend properly, i dont see how a rebuilt engine should affect your brakes.
thats a bit worrying really
