I check the endplay with no caps, and then recheck after each cap is installed. I do #3, or thrust cap, last. It is not uncommon to lose .001 to .0015 after installing the #3 cap. If you lose more than .002 after setting the #3 cap for maximum endplay, the parting line is not square to the thrust face. A good machinist will put a bearing in the thrust cap when facing the parting line surface during the align hone process.

I have had a #1,#2 or #4 cap hit the crank and limit endplay, as well as the parting line on #3 cap take all the endplay away. as stated in another reply start by removing the #3 cap and re-measure endplay.