how to align gearbox shift linkage?

[180sxdan]

I have recently taken out my gearbox, opened it up to inspect it, bolted it back up and put it in the car only to find the shifter can only move between gears 1 and 2, it won't go into any other gears. I started the car with the clutch fully depressed and it made an odd noise like something was rattling/rotating that shouldn't be. It wasn't a bad grind noise so I'm sure the gears are fine, also there wasn't any metal on the drain plug. But I'm going to remove the box again and open it up and try to put it back together so that I can shift to all gears with the box outside.

Is there any easy way to align the shift linkage inside the gearbox so be sure it's ok?
Or a quick way of doing it so I don't have to open and close the box hundreds of times to get it to line up.

I'd also like to know if this has happened to anyone else before.

Cheers.

[180sxdan]

After a bit of thought and research I realised the clanging noise must have been one of the dowel pins that were loose when putting on the pressure plate, once the flywheel spun I'm guessing the movement made it come out completely causing the noise. Or at least I think that's what's causing the noise.

My question now is should the gearbox be able to shift through all gears when the box is out?
I will be trying my best to align the housings so the shifter linkage is well aligned and I can shift through all gears but I'd like to make sure it should be able to shift between all of them fine meanwhile the box is out of the car and without oil.

Thanks.