Yes I have done this now and have 0.005”, more the issue is without caps installed I have 0.018”, which means all the thrust is taken by the cap rather than the block which in my mind is not ideal. More to follow
Take the cap side thrust bearing and clearance it with some 400 grit paper, re checking till you get the .0018 like the saddle side thrust bearing gives.
Fyi If you are using a stroker crank, you need a narrow main bearing set, the felpro full groove version, because the wider bearing keeps the crank from moving.