Now, I've got a TJ, not a JK, so my advice isn't model specific, but I did a bunch of research before herculining my rig and here's what I have to offer.
As for masking, etc. You get what you put into it. If you don't mind glancing down and possibly seeing floor that's not covered, then masking everything should be fine. I spent a little extra time removing everything (console, brackets, etc.) and putting a small piece of tape over every hole I didn't want to fill **as well as** sticking something to that tape so that I could later go back and find every piece of tape to remove. I don't regret any of the time and effort I put into lining my Jeep since everything is covered. If the brackets are going to be covered by the console, then masking the brackets under and making sure you spray all the way up to it should be good.
Your post about 120f temperature and location in your profile indicate your rig is going to see some very hot temperatures. I'd make sure you get something that will not melt or get gooey. I made that mistake on my old CJ.. as the outside temperature rose, and the floor would get hot from the proximity to the exhaust, the floor would get a little gooey and I don't live in places where we get 120 degree weather. I would think it would be better to get something durable. I bet you'll be happier in the long run.
97TJ, 6cyl, 5sp, 37" Krawlers, 6" RE long arm, too much more to list - visit my website www.jeffsjeep.com for more.