When you pull up that carpet to check the rust damage, if the metal still feels solid (as in you
can't put your hand through it) go ahead and apply an anti-rust coating. Use a wire brush to remove any loose rust particles, and clean the area. I used Eastwood Co.'s Rust Encapsulator on my Wrangler with good results. After it dries you should be able to paint over it if you so desire.
As far as the engine coolant temperature, do what's already been suggested in prior posts. Here's a website to look at if you're not entirely sure how to burp the system:
Jeep Cherokee Engine Cooling System - Burp Air System - Modification It looks like overall you got your girl a well-cared for Jeep. Congrats, and welcome to the Jeep world!