Yes, you can cut the T5 shifter near the floor and weld the stock shifter to the stub. That's how I did mine
here. At the time we couldn't post photos directly on the 'Bolt so member Lugnutz hosted the ones on the post above for me.
At the time I felt I needed a crossmember under the T5, I've since removed it with no problems cropping up.
I also took a different approach to the input shaft by doing a bit of redneck machine work. If I ever do another conversion, I'll use the Jeep input shaft Lugnuts has on his site, no reason not to and it's a very simple, smart solution to what some see as a complicated challenge.
Strongly suggest clicking on the links at the bottom of Lugnuts post and studying the info he freely shares.
Good Luck,
RonR