1990 KDX Right Side Large Engine Cover Problem

Hey guys, kinda new here so bear with me. So I just acquired a 1990 KDX 200 for $150 from one of my friends friend with the engine locked up in the bottom end. From what I was told, the guy I bought it from said that the person he bought it from got drunk and filled the tank with straight gas with no oil and rode the crap out of it. Piston was in pieces in the cylinder but with a stroke of luck, piece of piston wedged itself underneath the crank and the walls are ok. Removed it and everything turns like brand new. Now to the problem. I took the right side engine cover off to inspect the gears and clutch plates and now I can't get the cover back on. I lined up the Exhaust Advancer Assembly and the corresponding shaft that connects to governor rod/KIPS. I also lined up the Water Pump shaft and placed the cover on. Everything sits flush except for the area where the shifting shaft is located. I took a good look at the shaft and the claw like object that changes the shift drum and it seems to be a far down as it can go after tapping it. The spring did come off at one point and the shaft moved out a little bit but I put it back together the way it came off. The spring for the kickstarter also popped out of place but I put that back in its little hole by the outside casing. Any ideas why the cover would be stuck in the shift shaft area but flush every else? :bang:

Hey guys finally figured out the problem. It turns out that the claw that changes the gears on the shifting drum wasn't seated properly on the external shifting shaft. I guess when the spring came off and everything moved up, it came out of place. I put it back in its place by pushing it backwards and everything shifted down into its correct position. Cover sits nice and flush now. Thanks to hardwater49 for making the suggestion to check the shaft and the corresponding parts.