1996 Ninja ZX6R Starting problem (Kawasaki Ninja 600)?

I brought a 96 ZX6R home in a trailer but left it in 1st gear in the trailer because I didn't know any better yet. When I got it home it was a little difficult to get out of gear and into neutral. It seems to run and shift fine now BUT, sometimes when i try to start it it will be cranking over and then make a loud "clunk" sound and then stop cranking. The starter sounds like it's still trying but can barely get the engine to go. If I let it sit for an hour or so and try again then it cranks over fine and usually starts.
I'm concerned that I messed up something in the transmission or drive gear when I towed it home but if it wasn't for the towing issue I would just think there was something wrong with the starter. Anyone have any issue like this or any ideas ? Thanks.

I have the same problem 99zx6r but I only wait for a few seconds and it starts up with some throttle. have u found the problem/solution?