sometimes those cross pins in the layshaft will fall out on ya when ya try to slap on the first spur gear, the first spur gear has the one way bearing in it, i found it was easier to set up the shaft so pin runs thru side ways, it wont fall out then. and working the spur gear on is easier to do. thing is you shouldnt of had to use bolt to drive gears back on shafts. they go one easily with just a lil hand pressure. its takin them off thats only tuff part. if it were me, i would take it all apart again, with the bolts loosened as i mentioned earlier, start assembly again, making sure things are seated right, and use that business card idea as well between spur and pinion gears, then once you got everything to liking tighten all bolts down and check the mesh.
a bent backplate, if bend is in a spot the mount bolts wont suck it down to flat, might be rubbing the back of gears, thats something to look for rub marks on backplate when gears are off.