The R3 is probably the most comfortable bike I have ever ridden. You are new, so you are not used to riding. In time, you will be able to ride longer, and you won't have the discomfort you are feeling now. Sometimes my left hand hurts if I am using the clutch too much in-town, but that's about the only thing that ever bothers me. And it takes awhile before it starts hurting. Body position is important, but on the R3, it's really not a factor. The R3 is ridiculously comfortable and upright. Go ride an R6, and then get back on your R3.
You will HATE the R6.
The only thing I can say is.... keep riding!
You will HATE the R6.
The only thing I can say is.... keep riding!