The Service Manual is available online so you can do most of your own minor service work (oil changes, brake pad changes, etc.). Just whenever you are ready to do something, hop on the web site and search around for someone who has posted something about it.
It takes some work to void a warranty. In other words, don't worry too much about that. Now, if you are planning to add a blower or turbo, then you should worry.
My only concern for you is tire changes. Our beasts are not kind to rear tires and you will be changing them often. Invest in some good moly grease if you plan to do your own removal and install from the bike. Check with your local guy to make sure that he can handle mounting the tire to the large Rocket wheel. If they do M109 tires, he should be able to handle the Rocket's. Depending on your riding style, you may also want to scan over the Darkside forum for some strategies to address tire longevity.
I'm sure that if you have participated in M109 forums that you have seen suggestions for immediate mods to the bike. The same is true for Rockets. For instance, a headlight relay mod is highly recommended right away. Removing secondaries and some other performance mods are also common.
If you don't mind, update your profile with your location and some local R3 Owners might be able to answer some more questions.