I had aftermarket carpet and it was ill-fitting from day one. But if I did it again, I would have just lined it. Mine is now lined with the Monstaliner rollin stuff. Nice texture without being rough. I keep mats in the front for heat reduction.
I wheeled for 4 days at a Jamboree and it never got so hot it was unbearable. Yes, it got warm, but when it's 90+ degrees out and very humid, it's not a big deal at all. But I also rolled on my liner with about 4 coats so it does have some insulating properties.
I no longer have to worry about carpet mildew, dirt getting stuck in there and never coming quite clean. This stuff can be hosed then wiped off - dirt doesn't stick in the crevices at all.
(That last pic was before I reloomed all the wiring - I was just laying it out for the cleanest results).
As for smell, once I put it on, I didn't even bother driving it for a week (I have another vehicle) so it could cure and get the smell out. It was never that bad - the solvents to wipe the TJ down before starting smelled worse! With everything back installed, I have not noticed any smell - in fact it smells cleaner than it EVER did with the carpet.
I did it with the top off only because I wanted to line the tub rail. You COULD do it with the top on, but with the top off it is SO much easier to roll in. If you're going to spray it in, I'd remove it just to keep overspray off of it.