I've done similar itinerary and never had the seat cut into my thighs. I use a AirHawk cushion for long road trips. Try a sheep skin or a AirHawk cushion. Others are going to suggest a custom seat.
In mid July I plan to ride out to CO and want to do Pikes Peak. How is the road surface going up there? Any idea how long it takes to get there from Colorado Springs?
Don't we have another thread going on about this same question right now? Something about sore inner thighs? If the seat is set too high or just plain does not fit then have it modified or a full custom seat.
To address your Pike's Peak question, I rode up there almost 1 year ago and the pavement was very good the entire way. The toll booth is just a few minutes to the West of Colorado Springs off of Hwy 24. You cannot miss it, there are
large huge green signs like you would see on the Interstate telling you where to go.