For a new owner, I always recommend they pull the transmission at least the first time, to really check things out.
Yes, it is much more complicated and involved than simply sliding the tranny back, but you have the opportunity to check out so many other things, in the process.
For instance, you will be able to grab the input shaft (splines) and try and push the shaft in and out, to feel for play. A minute amount is O.K., but too much slop and it indicates some shimming needs to be done. How many miles on the bike?
My bike used to hate the rain. Then I replaced the stock spark plug caps with NGKs, and I've never had another problem.
My bike never had the crackOmatic coil (earlier model), so I've never had to deal with that.