Joe's right about the mileage, but I do think it's gonna be hard on you - not so much the motor. Breakin' it up into 11mi legs will alleviate much of the road weary problem tho.
Handlebars? Well - that and the seat is up to you, comfort is a highly personalized thing. I would very
much recommend getting one of those oversized, squishy saddles w/a spring suspension. I'm thinkin on swapping out my handlebars with another that has a bit more rise so I can sit a lil more upright...
Tires? With the amount of street riding yer talkin' about I would not only recommend street tires - but ones with nice wrap-around tread for cornering. I run the knobbies on mine and even tho I trail ride alla time I still think about swappin' out to streets. The wear rate with knobbies is horrible. they do increase vibration and slow you down jus a lil. Yet - still, that's not a huge deal or anythin'
Stink lika 2smoker? That's a badge of honor around these parts friend!
but no - not really once ya get yer mix right. It's true the stock exhaust ends right underneath you, but that too can be fixed in time.
Hope yer ridin' soon - if nothin' else it's great stress relief!