Rock Hard 4x4's crap roll cage pulled my side bars inward and hosed my tops formerly perfect alignment. The side bars have index holes that set the alignment and thus the sealing. They anchor on the windshield frame and can be moved via an adjustment screw, which is accessed through the upper hole on the "A" pillar trim cover. The other two bolts are the large ones on either side of the sunvisor mounts. With the tops installed and latched down loosen the front two bolts on each side and see if the tops settle into the seals. If the need to be pulled to the sides, tighten the bolts through the upper "A" pillar hole a bit. If they're too far to the sides, have someone push them in, or ratchet strap them a bit.
Rock Hard's overhead bar was too short and pulled my side bars in too far. I had to clearance the indexing hole on the driver side to get the top to seal.
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'09 JKRU. 4" Teraflex long arm, Teraflex R44 housing, Teraflex / Fox Resis, Poly Performance skids, Nemesis Billy Rockers, Nemesis flares, 37" ATZ P3s on 17" 5x5.5" Trailready HDs, Spyntec hubs, Teraflex BBK, Mopar BBK master/booster, Superior front & Alloy USA rear axle shafts, CTMs, Reids, Synergy drag link & tie rod, WTOR hydro-boosted steering, 5.38s, TF Dual Rate front bar, TF bumpers, Warn Powerplant, Tom Woods shafts, AA xfer case cable, Kilby canister relo, RH4x4 cage.