What about the sway bar links? Will they not need to be extended 2" bc of the 2" lift in suspension? Also, the shocks are in bind now with the axle so far forward. Is that normal? Will that be a problem? It is hard to imagine the axle moving that far back once loaded. If you measure, it looks like it could only move back one inch?
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It is fine.
You do not have any load on the suspension, and the leaf springs are at full droop, which, because they are anchored at the front and are attached to a shackle in the rear, (and a longer one at that, which again, is installed upside down) it is permitting the rear axle to swing forward. The axles on leaf spring vehicles do not travel strait up and down, but rather in an arc, and are limited (and exaggerated because of the longer shackle in your case) in this travel by the shackle. And, unless you plan on getting air under the vehicle (jumping it), this is a non-factor.
When you have everything else done; body on the frame, interior installed, engine installed, front and rear bumpers installed, etc, THEN go back under the truck and attach your anti-sway bar. You will find that it will be very close to where it needs to be and that your wheels will be where they were supposed to be.
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Do the sway bars after everything is done. Also I still reccoemend worrying about the alignment once you have the weight on the springs per spec.