You got it, changing the pulleys (like you changed the sprocket) will stretch the gearing out (as well as the top gear for highway cruising). I like the spread out gears. As for the warranty, I would not think it would impact it, but I would go and ask the dealership.
I would recommend the OP ask the dealership, like you said. Mainly because that's who you're going to go to if you need to get warranty work done. If they say no, you can always go back with the name of the person, date, and time you were told it would not be an issue.
There are legal protections in the US that prevent manufacturers from voiding entire warranties due to modifications and accessories. The funny thing about legal protections, though, is that you're going to have to be willing to hire an attorney and take them to court if push came to shove!
Naturally, if damage can be proven to have been caused by the mod it won't be covered. For example, if the drive splines coming out of the transmission became damaged, they could blame the pulley and not cover the splines. (I've never heard of it happening, but just a 'for instance
. If a fuel injector failed, they'd have a hard time blaming the pulley.
But, again OP; I'd ask the dealer. But I do know that people in the past have been able to debaffle pipes, replace pipes, and do all sorts of mods and still have un-related things covered. Mine didn't have a warranty, but I did ask the dealer about my wifes bike; what the warranty requirements were if we were to install aftermarket pipes or debaffle the stock pipes. They said the pipes would no longer be covered (a given), but the rest of the bike would be! That's in line with what the law says they should be doing.
Good luck, OP!
Oh, it's worth mentioning that very few folks have taken their 900's in for warranty work, other than a couple of recalls, and some stators on earlier models. These have been some incredibly rock-solid reliable bikes!