Yes, the best way is to remove everything, and measure, and figure the difference.
But as mentioned, plastigauge is what you would use in this case. Remove one bearing cap, wipe the journal and bearing shell with a clean, lint free cloth (I cannot overemphasize the importance of cleanliness), lay a line of plastigauge on per the instructions, replace the bearing cap (with the bearing shell), install and torque the fasteners, remove the cap and check the plastigauge against the standard printed on the paper sleeve the plastigauge came in (I cut a length of the sleeve a little narrower than the journal so I’m not trying to lay 6” of paper sleeve on it).
After making a note of the reading, clean the plastigauge with a bit of denatured or isopropyl alcohol, and after ensuring the journal and bearing shell are clean, apply some assembly lube and reinstall, torquing fasteners to spec.
Do not rotate the crank during this process, as doing so will smear the plastigauge and skew the results.
You will need to rotate the crank for each rod journal, to the bottom of the stroke (precision isn’t a concern, you are only moving the journal to a position where it is easier to access).
As I mentioned, now is the time to do this. All main bearings, and rod bearings can be checked, just only do one at a time. Work methodically, and remember, cleanliness is crucial. I’m confident that if you know how to handle tools, and feel ok using a torque wrench, you can do it.
Thanks for the information about the time on the engine.
I have to ask, why haven’t you engaged the builder about this? If I paid someone else to rebuild an engine, and it only had 100 miles on it, I would look to them to resolve it.