Rod bolts fell out!
I don't think tapping out the old bolts did anything bad, if you tapped them straight out. Seems like you could just put them back in. See post #26.
Since you have the pistons already on, then I can see trying to put in the old bolts. I would:
- Put them back in and torque the rod nuts/bolts without bearing shells.
- Measure the big end for roundness with a good dial caliper; if you are careful, you can get valid measurements of differences under .001"
- Inspect the nuts as suggested above