Late night at the garage yesterday. We also tryed the sanding trick to the bearings, put them on the straight table and rubbed against 400 paper and got now 0.009 without cap and 0.0085 with the cap. Also, now the thrust bearings are much cleaner looking, no black stuff on them anymore. I will mic the bearing halves again when I got more time to make sure they're ok.
I also found that if you have oil (20W50) between thrust bearing, it will eat up 0.001-0.00015 out of clearance when you move the crank just with you hands. Of course with a breaker bar or similar tool you can break the oil film out.