For the warrenty side of things im not 100% sure but i would suggest that you maybe take it to another dealer for the 600 mile free service, i know this could be far away but from the sounds of that dealer
i dont think many people would take it to him.
As for working on the bike yourself as you say your not a qualified mechanic which in yamahas eyes will mean anything you may have touched moded or done yourself can not be taken as proof or proper workman ship, meaning that will not cover you.
But i cant see there being a big arguement as long as all your doing are the normal service items like oil, filters, etc etc as these in most bikes are not were the problems arise from. Along with this i would keep a date of every time you do some thing with the bike and milage eg oil change and take maybe 5-10 photos each time you do something like this. Therefore if anything does go wrong you can say look i did X,Y Z by the book, heres the dates, milage, and photos for proof, and a normal bike should not have this wrong at that milage (if you understand what i mean!!!)
For me i got my R second hand from a local yamaha dealer and apart from buying the bike and parts from them would not take it to them to service, heard too many storeys of mechanics doing stupid things and also when the sales man tried to sell me the bike give me the usual sales jip about the bike being a bit single its got alot of lurging.....blablhlabl, i just said to him blanky, i may look young but ive read about the bike, they surge and at the begining that was to do with a faultly ECU etc etc..... his face said it all and he shut up then, let me test ride the bike and i was happy,3 yrs later and 42k miles ive done most of the oil changes, filters, etc myself but get a mechanic (not yamaha) to do the values as i havent learnt how to do them yet, tyre changes bearings etc.
Rant over .....happy biking