Well done!

I would try to forget one lap rides and make two laps your new minimum. Where you are now, however, two sounds like a bit much - I would consider something in-between for awhile.

Your time is on track - not sure if you are stopping for red lights and such. One goal might be to get that under an hour for a 13.1mph average speed. To get there, I would focus on the ratio of time you are spending in various gears. Try to save the easier gears for hills and get used to spinning a good solid gear almost all the time. To me, being a "fifth gear" rider (or whatever) makes more sense intuitively than focusing on time. The nice thing about having a route like that is that you can really track your results if you want.

You live in a flat area. I think most riders would agree that six percent is a legitimate climb but two percent not so much. By the way, in real numbers you total up and total down should match because you got back to where you started.

The pain thing is common to new riders. Bike seats are inherently uncomfortable until your butt adapts to it. Hand numbness is also a very common complaint.