<<<<88 YJ using stock spare tire rack.>>>>
Hmmmmm... you just found your first jeep mod... a better spare tire mount. Can you say "Swing-out tire carrier rear bumper"?
But seriously, look at where the tire hits the top. Can you adjust the tailgate stop? My tire carrier works great, but if the carrier isn't opened all the way, the hard top hits the jerry can holders. Sometimes it's just figuring out what is hitting and why, and fixing that problem.
Not dissing the above solutions, but think twice before moving that weight out from the tailgate. Those tailgate hinges (and the tailgate structure itself) were designed for a specific weight at a specific distance from the tailgate's surface. Toss in some wheeling bumps and some added leverage and you magnify that force a lot.
Street driving, stock tires, no problem. Gunna hit some bumps? Over time, it could be a problem. The tire's support is only sheet metal hanging on a couple hinges and a door-latch, after all.