did you replaced also parts of the transmission?? or maybe it is not the original countershaft of this motor... like you said, engine was in parts... possible that the shaft is from another engine or a later year .. would look the same, but could be minimal diferent
i had the same problem with an 85 kx 250 engine last year... a good friend bought it in parts and i should rebuild it for him... you get quite crazy, when after 5th try with complete reassembeling all parts to right direction , the countershaft would be still clamped by the engine cases . i had a 86 tranny laying in my spares. swapped the countershafts and it worked...
later we found out that the coutershaft in the 85 parts-engine was a from a 87 engine.. now it sits in my spares for my 87..
for me it looked that the pre owner had mixed it by taking parts out... sometimes all looks good, but little things can make the big effects...
and there is always a reason, why selling an engine in parts and not assembled..
I think everything is in place, Been looking through the manual and online. The 88 models on have a washer on the mainshaft that the earlier 86-87 motors don't seem to have.
Kinda stumped on this one. Is there another shim you speak of?
As soon as I tighten the last few bolts in the case around the countershaft it seems to lock in place.
It's literally the difference of 2-3 turns on the bolts and having the shaft rotating freely and being locked in place.
83-2004 use many similar gears.. but the shafts are diferent, because of the changed clutch-hub´s and so on. 83-87 tranny uses washers between snaprings and gears... 88 and newer has only snaprings that hold the gears on the shaft...
you could try to loose this added washer that you spoke off and sea what will happen. at least you can only try to get a 88 countershaft or a good complete tranny ...