After having everything fitted, 4th gear now works fine, but during clutching (before enaging the clutch, i.e before letting foot off the clutch pedal) 3rd gear sometimes doesn't engage fully and pops out. At that time we still didn't have a transmission jig to adjust the shift forks properly. So the best was to eyeball it while everything is in, not very accurate since everything can still move around.
Before re-tearing down the transmission, the stop plate was re-adjusted to see if we can get 3rd to engage deeper, didn't quite work. During that time the little shift bushing in the tunnel was also replaced, this helped to remove alot of slop the shifter was experiencing, the shift coupler was pretty new and had no slop, so that was ok.
After replacing the shift bushing, shifting was now alot tighter, no more looking around for gears.
There was a new problem though, sometimes during downshifts from 3rd gear to 2nd, there'd be a little grind, almost like it was hitting reverse, but the stop plate is already well adjusted. At this point nothing more could be done without having a transmission jig, so we bit the bullet and got a cut up pinion nut type transaxle housing to use as a jig.