I am actually a loooong way from replacing my interior but I am getting ready for reinstalling the engine and transmission.
One of the things I saw that HAD to be reinstalled before the transmission was the front support bracket for the center console. It mounts via 2 studs that go down through the tranny tunnel and is secured with nuts and washers. I am pretty sure there is NO way you can get to those nuts in the space between the tranny and the drive tunnel. GM did not have to worry about it because the interior was all in when the body was mounted to the subframe on the assembly line.
So how in the world do you intall a new front carpet section with that bracket in the way????
2012 Mustang Boss 302 #1918, Competition Orange. FGF replacement 2006 Mustang V6 Pony, Vista Blue. Factory ordered. 2019 BMW X3 (Titled to the wife, but I'm always driving it for her. So I'm claiming it) Old projects, gone but not forgotten: 1967 FB 400, original CA car. After 22 years of work, trashed by the guy who was supposed to paint it. I had to sell it. 1980 Turbo Trans Am 1970 Mustang fastback, 351C 4Bbl, auto 1988 Mustang GT, 5 speed 1983 F-150 4x4, built 302 1994 Chevy K2500 HD 4x4, 454 TBI
Option #1: Remove Tranny. Option #2: Drill out / Cut off studs and replace with a nut and bolt. You can reach through the hole in the tunnel and position the bolts then put the bracket on and add a lock nut and bolt. This is how I did mine. You need the shortest bolt that will work since you have limited space between the tranny and floor pan. Put the bolts and nuts in prior to carpet install, then just make small "X" on each one and pull them through, then add bracket.
Now you may still be able to use the stock bracket studs and put the nuts in from the underside, but I'm not sure since I am using a Tremec 5 speed transmission vice the stock, so not sure about stock clearance.
...or you cut the carpet around the bracket. That's what I did. As you described, I couldn't get to the nuts on the underside of the tunnel. I cut slots in the carpet and dropped the carpet over the bracket. It's all hidden by the console anyway.
The factory carpet was cut to accommodate the front console bracket and the bolt hole for the rear. The cuts will be covered by the console. That's how I did mine as well.
When I installed my carpet this summer, with the transmission in, I was able to lay the carpet down, poke a couple of holes for the console bracket studs, drop the bracket in, and laying underneath the car, get the washers and nuts on the studs and tighten them down. With a little patience and a small selection of different wrenches, it can be done.
The console sits down on the carpet better if you cut a slot around the bracket. However, you can get the nuts on the bracket after the transmission is installed. It's just real hard.