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Will I be able to align it with no problems with a BJ flip and only 1 to 1.5 inches of lift?


yes

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I'll have more downtravel (assuming I don't end up over extending the shocks...hmmm, spacer at the top of the shock mount?), but I'm asking is it really worth it for such a small amount of lift, or should I not bother?


Your shocks will be ok.


Curt B 89RS Calmini Header Delta Cam 33x10.5 BFG MTs & 90 Trooper 3.4 v6, SAS D44 ARB/Hobart 5.38s 35s my pictures