Hi,
moved this into a new thread and out of the FAQ section.
It's a bit hard to say what the cause is but I think in any case you're going to need to remove the box and open it again.
Just one thing though, if you disconnect the gear linkage from the shaft on the box, can you select any gears by just moving the shaft on it's own? It should pull in and out for 3rd & 4th just using your hands.
It could be as simple as the ball & cap on the linkage inside the box not being located properly, when you put the box halves back together you have to make sure these line up. Or a part of the shift finger mechanism could have moved but that seems unlikely. You said about clearing the crud out of the box, what crud do you mean? It should be clean in there aside from perhaps old oil. If there's anything else in there something could have got stuck in synchro ring on the gear itself. But really, if there's any debris in there then it's total strip down & wash everything in a parts washer time. Even tiny bits and pieces in there will cause damage.