Suspension is done, engine is pretty much stock (which is fine), next year maybe full exhaust and mapping, so this year is either brakes or rims (unless I am missing something else). So..are brakes the better way to go first? Or would they both be about equal. I am leading towards rims, hoping it will maybe help the bike respond a little better, maybe a little less effort throwing it around, better acceleration/deceleration?
What is a PVM?
PVM is a rim company. They are just one of the few i would trust to buy from.
Im not sure what your looking at for brakes but it shouldnt be a ton of money to do it. Stock setup is pretty good. Some new lines and your almost done. I use ebc HH pads on my race bike with radial fronts, brembo master, braided lines and floating rotors. Thats about as hard core as you can get and its not much money. On the r1 id skip the full floaters and keep oem calipers, probably skip the new master too. Maybe pads and lines and you should have fantastic stopping power.
You can kind of feel the rims everywere. I had to redo all my suspension settings and changed the angle of my clipons to compansate for the flighty front end i had after i put them on. Everything was pretty much improved. One thing i will warn about getting aftermarket rims is make sure you can get sprockets easily. I have a few friends with rims that take many, many weeks to get sprockets in so they buy in bulk. When i first got my pvm they were new to this country and it took a few months to get them, now i can have them tomorrow but it did screw me abit in the beginning.
You should also plan on getting new bearings with the rims. Id go ceramic but they are pricey. I never really noticed the difference on the street or track even since i did them with a few other thing but i definately noticed them when i would stunt the bike. When i would do rolling stoppies on normal bearings i would roll maybe a hundred feet and i was really trying, after the ceramic that distance doubled and then some. It actually scared me the first time i did one because i didnt think it would make a difference. Having the bike on the stand and spinning them by hand they go much, much longer and are smoother too.
What have you done to your suspension?
Im also not a fan of any real engine work but bolt-ons should be done before the rims. Things like exhaust and tuning will net bigger gains than the rims. If it was my r1 and i was in your shoes with your bike id be looking into easy bolt-ons and as much weight reduction as is affordable and easy. The key to these r1's is to get the curb weight down. Rims help but there are things to do before hand. Exhaust can be almost 20 lbs just by itself. A nice light battery can be another 10lbs or more. You really want to try to get to as close to the other liter class bikes as you can in both power and weight before going for big ticket items.