Another thing you should keep in mind is that you've only been riding for a week or so; it's something you'll get used to. I used to feel the same way as you when I went from a '93 F2 to an '01 F4i, but after a few days of being sore, I got used to it and was able to do some pretty long rides. Of course I'm only 5'6", but the same concept applies as your body gets used to the bike's position.
Surprisingly, I wasn't sore after I rode my '03 F4i back from the dealership this past Thursday. I rode 70 miles, mostly highway, after not riding for 9 months. I stopped to stretch once, but was okay otherwise. Compared to a lot of the supersport 600s (i.e. 600RR), the F4i is pretty damn comfortable.
'06 Honda CBR 1000 RR -
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