the pin I am referring to, I believe is the same one you are calling as "holding pins back down into valve body on top of trans". if the valve body is not in the correct position (forward to back, and properly rotated to one of 2 possible positions) the pin may fit and screw in but not be in the hole that is the same size (not a slot, but a hole machined to the same diameter as the pin) in the valve outer housing.
however, if you have removed the wires from the same valves, and it stays in reverse anyway (no neutral), then you have a problem in the clutch packs.
if what happens is that once you have gotten it in a gear it sticks, it may be in the sam valve.
Early versions had the cap and pin as separate parts, and the pin could fall down through the valve and get caught in the gears below it, later versions used a different Sam valve scheme.