Congrats on getting it started.
On the noises: I have similar concerns as you do. If my daily driver had some of these noises, I would think something is wrong. I have driven it about 300 miles since the re-furb. I am getting more comfortable with the strange noises, but I am looking forward to the May Super Cruise gathering in Golden. I will get to hear a few other Jeeps and their noises.
I did change my oil after the first 100 miles. I was running 5w-30. I switched to 20w-50 high mileage + a ZDDP additive. The engine sounds better with the heavier oil, but I think I'm giving up some gas mileage. My front pulley wobbles a little. (New from Walcks) It causes a little engine shimmy. My transmission wines a little in high gear, but not so bad that it's annoying. Add some rattles in the passenger seat frame while driving by myself, and I'm pretty sure I won't be sneaking up on anyone.
On you wife's concerns, my wife has gotten more comfortable with the lack of constraints. When I am in the passenger seat, I spend half my time looking for something to grab.
Tim