If it shifts that difficult it may be a bent shift fork, just rebuilt the tranny in a 450yfz having the same issue. Thats what we found to be the issue, shifted wonderfully after the new shift forks were put in
Sounds like you need to get to the carb, running it empty may have ran a blockage into one of your jets. There is also the chance the fuel filter is plugged if it has one.
You have to have the 2 holes that are in a line on the cam on the top center and the dot on the top gear top center and line the dot on the bottom gear up with the arrow above the gear to line the bottom gear up you have to have the clutch assembly off. Just remember everything has to be top dead center, I think you pull a side plug to check top dead center of the crank.