Great questions! Something I've been thinking about all morning. I believe the cause was due to the wrong crank pulley spacer. I used the DE oil pans, and crank, with a VE block. I didn't notice much wrong with the car until a few months ago, when the alternator was shredding the alt/crank belt. The alignment wasn't correct, as you could see the crank pulley "wobbling" slightly. I decided to just let it be, obviously a HUGE mistake. Plus you could see the alignment was off from alternator to crank by 1-2 teeth (a few mm's).
I believe that movement in the crank caused the first rod to either: 1) crack, or 2) lossen rod cap bolts, as a slight vibration over thousands of miles and constant revving to 6-7k rpms.
I never did go back to see what spacer I used, as I think it was the ve spacer, not a de spacer. I think there's 3 different spacers.
That's my theory. So...user error.