I just put on the 3.25" lift and ran into this problem while running the t-case drop aswell.
You will need to re-locate your center console back about and 1" to 1.25", redril mounting holes and snugg it down.
Also you will need to do the following. When the console is removed you will need to remove the lower rubber boot from the jeeps floor (tub), once that rubber boot is taken off you will see your 2nd problem, your shift lever will be hitting the tub b4 it fully engages into 4th gear, chances are your 2nd and R gears are not engaging fully too.
So the best thing to do is remove the dust seal on the shift lever down on the transmission, there is a hardened stell cup under that dust seal that has an oval shape cut into the top of it. Push that cup down and rotate it counter clock wise, the easiest way to do this is from under the jeep with one arm on one side of the tranny and the other arm on the other side, looks much like a big bear hug, push down and turn that cup.
There is a spring under that cup so once it is turned/released it will pop up, you will be able to then pull out your shift lever out, from the top of your tranny.
Now that your shift lever is out of the way you can trim your tub with a grinder, sawsall, jigsaw etc... you only need to trim about an inch out of the tub, your rubber boot that attatches to the tub should still cover your altered hole when finished. Note, when grinding the tub make sure to cover the hole in the top of your tranny, the hole that your shif lever came out of.
Once everything is back together:
Tub trimmed so shift lever does not hit
shift lever re-installed
Console relocated back 1-1.25"
you are all set,
its possible that your shift lever will still hit your console, so you could take it back out and tweak it forward a bit so it will no longer hit.
its a little bit of a job but took me about 1.5 hrs. figuring this out as i went along.
Maybe take some pics