'came out during brake in process' - hmmm? How do you know that? Did you tear the engine down prior to it destroying itself?
'pins are tight now' - how tight? Press them out and measure the little end bore and pin to see the amount of interference. The fit has to be loose IMHO. Perhaps someone can help me out here, but IIRC there should be approx 750-900 lbs of pressure needed to press the pin into the rod. Also, how tight were the pins in the pistons? Did they pass the gravity check of holding the rod at 45 degrees and then rotating 180 degrees and the piston falls to the rod?
Lastly, if you didn't have piston to valve or head contact, then this is nothing that you did. Again, my opinion. But if what you're describing is 100% accurate and this happenned to me, then the guy/machinist I use would step up here.
Could really use some more pics to confirm - head surfaces, bearings - both rods and mains, bore (unless undamaged) and piston tops and skirts.
Jim