First, on the stock tires, I used 70 psi. I have always thought that near max inflation is best to avoid flats. Don't know if that is accurate, but it seems when I was mountain bike I got it flats I got were always on those short rides where I didn't check or top off my pressure. As you may remember I actuly went the oppset of most and went to a smaller higher pressure tire. I run them at 110 but I almost never leave the pavement. I use the padded underwear. If I'm just going to zip into town or something I don't brouther but on long rides I put on the padded underwear and wear my normal (baggy) shorts. When I used to ride road bikes, I always wore bike shorts and dint wear anything under them
It maybe all in my head, but I think the bike takes time to break in. I m sure it gives me less road vibration now then it did a couple hundred miles ago when new. I did a ride with some road bikers today. 50 miles and I had no problem keeping up. Yesterday I did 35 miles with a "slow roll" group. I felt comfortable in both groups. I did adjust my seat a little lower for the slow ride group to make it easier to mount and dismount, but no big deal.
I have a little wedge bag under my seat. I keep and extra tube, CO2 inflator, plastic "tire irons" and one of those zillion function multi tools. I don't think it matters which as it just for eng use. I know some guys that think that is their tool kit to work on the bike. They are often disappointed. I also have a couple of unused zip ties in there, never know if you might need one for some reason. Of course I have a computer and one of my water bottles mounted up on my bars.
When I was riding with the slow roll group, I went down to my smallest chain ring for the first time. Later when I tried to shift back up, it just kept grinding the chain. Stupid me, I figured out it helps to get in you smaller rear cogs before trying to go up the chain wheel. I haven't really looked at it yet, maybe a little adjustment or possibly the cable is hanging up. At any rate I'm sure it will be addressed when I take it back for the 30 days check up