ok, i checked two different motors, and the rod with the ball bearing behind it sticks out 9-10mm from the end of the shaft. from the pictures, it looks like your's sticks out further.
i don't think tapping it with a hammer will help because the way the shaft is made, it's sandwiched between to pressed in bearings, and there isn't any play between them for it to slide back and forth. there is a tension sdjuster on the clutch plate side, but if you didn't mess with the shaft, it shouldn't have moved. and even if it did, i don't think it would alter the length on the sprocket side.
i think your problem is as simple as tightening the flower nut down more.
there is a heavy duty spring around the shaft, and that needs to compress to pull the clutch in. the only way it'll compress is by tightening the flower nut. i know when i took mine all apart it was real tight and i had to use pliers to keep turning it.
to break it down, when you pull the clutch lever in on the bars, the cable pulls the lever on the engine.
the lever pushes against the rod and ball in the shaft, which compresses the spring.
with the spring compressed, the shaft pushes against the flower nut, which is connected to the clutch plate.
the clutch plate moves away from the flywheel and pads, and disengages the drive of the engine.
more or less.
so right now, working backwards, the clutch plate and flower nut isn't compressing the spring on the shaft enough, causing the ball and rod to stick out too far.
also, on my first motor, the clutch cover didn't fit flush after i took it off. it felt like it was spring loaded. it came off that way. i just started all three screws, tightened them evenly, and with a little force, it all went together. basically, as i tightened, the clutch arm was pushing against the rod and pushing the spring in. worked fine, but that clutch was always hard to pull, right from the start.
so, i'd get a good grip on the flower nut with some pliers, hold onto the flywheel as well as you can, and tighten it as much as possible.
should work...