While in the process of doing a major maintenance on my bike in preparation for the coming season (and because some of the major maintenance items were due anyway), I recently changed the sprockets and chain of my '02 GSX-R750. Following the maintenance manual, I removed both sprockets, cut the chain, and then remounted all three. During the installation of the front sprocket though, I ran into trouble trying to torque the mounting bolt on to the specified 83.2 ft/lbs of torque because there wasn't any resistance from the engine. The maintenance manual makes no reference to putting the engine in gear or any other method of mounting the bolt, just that it needs to be at the specified torque. Remembering that 1st gear has a lot of resistance, I popped the bike into that gear and again tried to install the bolt. I still couldn't get enough resistance from the engine to install it, except this time when I got close, the wrench seemed to slip and at the same time make a sort of clicking noise. Eventually, decided I needed to install the chain and then use a pipe through the wheel to lock the sprocket in place, which ultimately worked fine.
I would have thought nothing more of this situation, as I thought that the clicking noise was just some slipping in the clutch or something like that, but when I told one of my friends who has experience doing these jobs, he told me that I might have sheared off some of the teeth on my first gear. He said there was no way to tell without starting it and running it up to a few miles per hour in each gear, while on the rear stand, to see if there was actually any damage, so I did and it seemed to run normally, though there were some sounds coming from the area around the sprocket that I wasn't familiar with. First, when in 1st and 2nd gears, when I released the gas after running it around 10-12 mph, there was a repetitive clunking noise that died out after 3-5 repetitions. Then, when I ran it a little faster, I got a similar sound from the same area, only much faster. There were also some other, random clunking sounds that would come, but without a predictable pattern. The problem is I can't tell if the sounds are related to damaged gears, additional chain lash due to being run on a rear stand rather than on the ground with my weight compressing the rear shock, an improperly adjusted chain tension, or even the fact that I didn't add more chain lube over the prepackaged grease already on the chain yet (I know this is a must, but I didn't ride it yet, and I only ran it for about 5 mins, 2 of which was warmup with no wheel movement to make sure the oil was moving in the engine).
I'm hoping that someone here has experience enough with this situation to be able to tell me 1) if there really is a chance that I've sheared teeth off my gears and how likely that is to have happened, 2) if I did, what symptoms should I really be looking for, 3) whether the noises I described are, or could be, from damaged gears, 4) what other alternative causes are there for the noises I'm hearing, and 5) is there any way to be sure that did or did not damage the gears without actually breaking open the gearbox to visually inspect them?