I had a similar issue when doing the bearings in my nephews KX85 a couple weeks ago.
I had the engine all back together, everything seems right, but even with the engine in the frame and chain on, I couldn't spin the counter shaft with the rear wheel.
So, I took it back out, split it again, and inspected. I couldn't find anything wrong. Nothing. It all looked perfect.
So, I put it all back together, took my time, making absolutely sure nothing was wrong, and put it back in the frame.
Same issue. Very tight feel.
I figured it must be that the bearings & seals and whatnot needed to seat, so I just let it go.
Got everything back together, fired it up. Engine sounded fine. Ran like a cut cat..
I took it out in the yard, just to test it's pulling power.. felt great.
Put the bike back on the stand, gave the rear wheel a good shove, it turned nice a freely.
So, something must just have needed to seat properly after splitting the cases.
I'd say if you put it in the bike and it runs fine, let it be. Just my guess..