Its strange that you could find all the gears while the engine was on the workbench, ie not running (I assume) and without the use of the clutch?! was the gearbox re-filled with oil after the rebuild? why was engine re-built, had it done high mileage? if so, were the gearbox internals measured/checked for wear such as excessive end float, chipped teeth, bent selector forks. Has the gear selector shaft had a knock and is tight in the casing. Maybe somethings been left out or not indexed properly, sounds like another tear-down to find out.
Chris P.Duck
May 2010