As much as it SUCKS, I highly recommend leaving the room and just leaving him alone for at least a few hours. I just got a new baby yesterday and it's like TORTURE not spending every second in there staring at him, but it really will help him settle in and destress.
As for your substrate, you mentioned looking for the Repticarpet, but I just wondered if you'd read about the virtues of using non-adhesive shelf liner. I seriously should get a commission from those people, because I endorse it so much! I just love it because it's cheap, disposable, easy to cut to size, and super easy to clean. I use Duck brand EasyLiner, which I get at Walmart for $6 a roll. I chose that brand specifically because their solid colors don't seem to have any kind of "chemical" smell to them? I noticed any with printed patterns and some of the other brands have kind of a noxious smell that worried me. It's important to get the non-adhesive kind, because the glue from the adhesive kind can heat up under the basking light and put off some toxic fumes. Anyway, that's my endorsement for shelf liner. You can see how the taupe color of it looks in my viv by clicking the link to my webcam in my sig.