Do I torque the control arm bolts at ride height with weight on axle?

Try hand pressure to compress the driveshaft back to where it was. Grease pressure inside can cause it to expand outward on its own.

I hooked up at ride height, trying going full droop and it stopped the axle about 2-3 inches short. Bumps are centered. Should move the axle forward or get a new shaft?
 
Sounds like a new shaft would be in order if it is truly too long. Moving the axle forward is great if you can do it. But cycling your suspension with the springs out and track bar disconnected will likely reveal some clearance issues with even less than an inch of forward axle movement. For example, the frame side of the front track bar against the differential. Also, if you run a shaft that's too long, I'd worry about damaging the transfer case amongst other things.
 
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I am using the Currie bump stops, when I set my lower ca length was I suppose to center with bump stop extensions in?

No, you cycle without the bumpstop and center it on the spring perch. Then set your bumpstop for either shocks or tires, whichever hits first.
 
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It sounds like you are fighting your links binding. Disconnect the pass upper link and see if it moves easily. When you are done adjust it to fit.

The upper link brackets are weak. You want equal pressure on them,in both the front and rear. Not equal length uppers.