I am checking the deck height/clearance on my /6. I am using the acid core solder method. I am placing the solder inline with the wrist pins. Do I have to have the rings installed when I do this? It would be much easier to change the cylinder shims if I didnt. I realize that the Pistons will not stay perfectly perpendicular to the cylinder wall but if I am online with the wrist pins, would it really matter that much?

No

Check both sides of the piston.

My first checks revealed that my registers needed to be "trued".
The registers are the flat surface that the cylinders sit against on the case.
The measurements after the machinist were more consistent.

Just for grins, here is how I did it:

While it is easier and physically possible to check deck height without rings, I always use them. Why? Because Its important to have all the things in place that could create variables in the values you'll achieve.

Without rings, the pistons won't to flop around in the bores, and its tougher to get repeatable values. Take the time to be as thorough as possible, thats the mindset that an engine builder must have.