Sparky, put your magnet base on the pinion snubber pad of the housing & set it up on the bearing caps. Ping it a few times to make sure it zeros then check the other three. If you have an odd cap joint, check them in pairs. If you have any more than .005 or .006, reseat the jiont & check it again. The tube is only relevant to the the accuracy of the fab & is normally balanced out.
Trans shaft/pinion angle are critical being that close together & I see you have a "fine china" Harbor Freight angle finder that I consider a ball park gauge. Better off to make up a dummy shaft to go up the back of the trans & through the pinion bearing races in the diff. You're going to have to be right on the money with the crank centerline but this way you know it's right on.
On a build from scratch, it's best to put the whole package on a center bar & build it in. I don't know how you did yours, this is more of a general info statement for others.
I envy you having many hands in your build, it sure speeds things up.
Sid.