Did you keep the rods and caps together? If the align boring isn't happening then the first thing I'd do is remove the rods and take off the main bearing caps. Plastigauge the mains after torquing to spec and see if the crank turns freely. Make sure the clearances are within spec. All the clearances, not just one or two. The notches on the bearings go on top of each other, same side or whatever you choose call it. Hopefully the rods were marked 1 thru 6 and the caps were kept with the correct rod. If not you'll need to have an automotive machine shop check that for you and put them all back in the correct order, resize or whatever.
Install the rods in the correct position and one at a time check clearance with plastigauge and check for an easy rotation. If any rod causes a tightness problem stop right there and you'll have at least 2 rods and caps screwed up. There should be an arrow on the top of the piston and that points to the front of the engine. That will tell you about the bearing installation. Good luck.