Whilst that gearbox jig in the picture above might seem like a useful tool, the best jig of all is the actual engine and gearbox components themselves, as no two are exactly the same. They can take the same fettling as a timing chest to get all working ok...............Try setting up the gearbox after you've machined 20 odd thou from the mating faces of the cases, that takes some sorting due to loss of running clearances (end float). It sounds like your cover plate layshaft bearing is not fully home, perhaps the shaft is a bit too snug in the bearing and when you remove the cover it is pulling the bearing out, lininsh the shaft a small amount so it slides into the bearing without grabbing. Try installing the cover plate with just the lay shaft in place including it's gears and with the input shaft removed, put your finger through the bearing center to see if the layshaft spins freely and fee some end float on the gears. if you isolate things like this, you can sort where the problem is.