I have an older TM, but I think I can still answer your questions. People with newer TM's, please correct anything that has changed that I don't know about.
There have been numerous reports of bad valve stems in previous posts.
http://trailmanorowners.com/forum/sh...ht=valve+stems
As far as I know, you are not supposed to jack up the TM (of any vintage) under the axle. Are you sure that they didn't jack it up under the frame? It seems that an experienced roadside assistance person would know better. You'd have to get around (as in towards the center of the TM) the tire to jack it up by the axle. The frame is right behind the tire.
I don't have a lift kit on my TM, but from what I've read the newer ones like yours already have one built in right out of the factory, so there is no need to remove the "skirts" or "fenders" as you call them. If we change a tire we have to remove the "skirt". If you need to remove this you need a special tool, it's just a square driver. You will need this driver to take out or replace most of the screws in the TM.
Our water heater is gas only. I'd imagine that if yours is both gas and electric, when the electric element is on, the amber light would come on. If it's on gas (which it would be if you're dry camping) then it wouldn't be on.
Sorry to hear about your tire changing problems on one of your first trips! At least it didn't take you long to get back on the road!
Hope you are enjoying your TM. We're looking forward to our next trip to the TM rally in Petaluma, CA.