I a running a new JE Reel 1310 HD shaft now with no vibrations that I can tell. Sitting in my driveway, the shaft reads 13.5 degrees and the rear diff reads 14.5 degrees. This results in a slight upward angel of the diff to the shaft. To make them equal, I would need to drop the pinion (lengthen the rear uppers) by .5 degrees.

Should I worry about them being dead on, or is it worth turning the uppers once to lengthen them. I am wondering if even just one turn of the heim joint would result in the same difference the other way (angle down) rather than equal.

 

Your diff is at a greater angle than the driveshaft?

 

Yes, by 1 degree, which means that the upper control arms need to be lengthened slightly to make the angles equal.

I previously had a 1310 OE replacement shaft that used the stock flanges. The new shaft articulates closer to the transfer case and differential due to replacement flanges. This made my previously "perfectly straight shaft to pinion angle" slighly off.

My question is whether the one degree up is a problem, or would one degree down be a better compromise if one turn of the hemi joint on each of the upper control arms couldn't hit the angles dead even.

 

Mine is opposite. My diff is a couple of degrees less than the drive shaft. I think lesser angle on the diff may help prevent starving the pinion bearing of oil ( I don't think this is an issue with your small angles). My TJ angles were in the 20's.