Measuring External Thread As a Cylinder

Measuring External Thread As a Cylinder

Hello,
i wanted to see some opinions on the best way to measure these features. They are threaded studs that extend out from the sub frames we are currently making. There are a total of 12. 4 of them being m10x1.5 thread and 8 of them being m12x1.75. The 4 M10's have 2.5mm positional callout to datum and a 1.5 composite position call out to each other. I currently measure them as cylinders (3 sections with 5 points per section). I then use centerline of cylinder and construct a circle onto constraining plane. 

I use the circles to check my position call outs. Everything works fairly well except i will randomly get a cylinder that was interpolated incorrectly. It may have a severe angle or even seen once the cylinder was created at 90* from actual parts. This is bad because if it thinks the cylinder has major deviation it will not allow me to report any of the GD&T related and also does not export the data for all cylinders related due to being reported as composite.

I am using a 4mm ball probe and just probing the threads currently. I thought about making some machined collars to thread onto threads and probe that instead of threads. 

Just wanted to see CMM-M opinions first and decide what would be best options.

Attached is screenshot of drawing showing call outs of threads locations.
Thanks