Will got a new job and moved from Brunei. The bike was too much to take with him internationally, shipping isn't cheap and vehicle laws change.
Why did it get disassembled originally? Did you go in to just replace the KS pawl and some gear guts fell out? I think that's what happened to Will.
There are no guarantees here. The gearbox-in-the-frame reassembly takes some finagling, but many others have done it. The inner cover has bearings in it, so it holds shafts in correct alignment and provides correct end spacing. With the inner cover in place and snugged up you should be able to roll the rear wheel and operate the gear selector. If it's rolling freely, you can hit neutral & have all 5 speeds, you are likely there. Then you final reassemble and CAUTIOUSLY test ride.
If it was stock & worked before, and you just replaced part-for-part, it should work if you haven't flipped something over or transposed a position. Test shaft movement by rotating them as you reassemble. Axial play also can't be excessive, make sure any & all shims are in place. The gearset can't be allowed to "bind up" and go solid when you tighten down the inner cover, castings get cracked that way. Sometimes a soft-faced plastic mallet is needed to tap as you go to help the internal bits settle back in.
Just like a doctor, "do no harm". Study the exploded views carefully & test as you go. It's just a monkey puzzle, right?
...and don't forget any gaskets!