You're not being a wuss. Even though I have not ridden a diamond frame bike for over 7 years, I ride a recumbent now, I still remember what it was like to dial everything in perfectly so my crotch didn't hurt. The problem was though my crotch did nto hurt too often the rest of me did regardless of how well I adjusted or changed things.
It will take time to adjust everything and may involve a better saddle. Let's start with are you male or female. I am guessing by the way you describe your discomfort you're a guy. My second question is did you bike shop do a fit kit with you to make sure the bike is best matched to you. Did you just simply take this bike for a spin around the block outside the shop and liked it so you purchased it?
If you would please answer these questions and then I think it will be easier to proceed from there.