won't go in gear

The issue is not with the transmission.

When you walk the car through the gears while it's not running, it does move the input shaft and the clutch disc that are splined together, slightly. If you can't, as you've stated, something is locking that clutch disc/ input shaft assembly. That's why it's not a problem on the bench.

Something is interfering with the clutch and input shaft. The dead giveaway is the reverse problem. Think about it. If the car is on the ground, everything is put together, engine is running and the clutch is supposed to be disengaged, so the input shaft/ clutch disc are at a stand still, there shouldn't be any motion to cause a grinding sound of any kind.

If you can't get the gears in, with everything installed and the engine off, the clutch/input shaft assembly is locked solid on something that won't even let the synchronizers bump it over a tooth.

Button the transmission up and leave it on the bench.

Pull the bellhousing off, pull the clutch and flywheel off, use a dial indicator on the crank and index the bellhousing, according to factory process and recommendation with the offset dowels.

If you get so much as .002" side load on that input shaft, from the bellhousing not being directly centered on that crank, it will do the same thing as not having a big enough pilot bushing.

Any interference that you have on the input shaft to pilot bushing will rub and make the input shaft/ clutch disc assembly do whatever the crank is doing and not allow it to do what it needs to do on it's own.

If you used another input shaft for an alignment tool, odds are, your pilot bushing diameter is fine, but the suggestion above, stating that you need to be able to put the transmission flush with the bell, without any help from the bolts is absolutely critical.

When you center the clutch disc with the input shaft, it does center the clutch disc in the pressure plate against the crank, but the transmission centers into the big hole on the back of the bellhousing. If that hole is not exactly centered on the crank, via indexing dowels with the correct offset, clocked properly, the trans does whatever that bell does and fights the crank/ pilot bushing.