From your measurements of 3.999 to 4.008 you have .009 clearance and .006 there. That would indicate the piston has been rocking in the bore. A piston to cylinder clearance should be about .0025 new so you have a clue there as to why you have blow by as the rings would expand half way down the bore and then contract at the bottom. If it were mine i would go to the next oversize piston and look for some decent clearances. If you hone again and take out another .001 you will increase that clearance.
Hope it works for you , good luck.