I assume you think you think you need a custom boot because you have difficulty keeping your transmission in gear. The pic you posted looks like a stock shifter boot.
If you still have the inner boot in place, you might get the necessary clearance by removing it.
I have a body lift and it causes the same problems as a transfer case drop.
Some Jeepers report difficulty keeping their transmission in second, fourth and reverse gears. For me, only reverse gear was a problem.
My cure was to grind away the rear of the shifter opening as close to the screw holes as possible without actually grinding into the screw holes. I left the inner boot off.
Second and fourth gears are just fine now. I still have to hold the shifter in reverse. It isn't a big issue for me right now and I will cure it when I get rid of my current transmission for an AX15.
There are some companies (or at least one) that make custom leather shifter boots. Before spending the money on a custom boot, make sure that your problem isn't caused by your shifter contacting the rear of the opening in your floor.
In order to access your shifter opening, you will have to remove your carpet and your current shifter boot. Post a few pics of your current setup so one of us can give you better suggestions.
Good Luck, L.M.
1987 YJ-4.2L-Standard Shift- Re-manufactured Carter Carb-2" body Lift-31X10.5X15 BFG KOs-188K Miles
HEI distributor with computer and all related relays and wiring removed.
No back seat.
12K Badlands winch with dual batteries.