I appreciate the input folks. Like I said, I haven't ruled anything out. Honestly the only reason I'm even looking at doing the rod bolts is because Henry recommended it. I have searched high and low and the only real mention of rod bolt issues come from Wayne in thread here on PP and Bruce Anderson's book from what I've found. I'm not saying they aren't a weak link, I'm just saying if they are, there would at least be one thread somewhere on the internet with proof that the bolts failed.
From my searching, I've found exactly two threads where guys said their rod bolts failed. One, the engine was rebuilt and the original bolts were reused... so no real surprises there. The other, the person blamed the rod bolts but when he posted pics of his rods, there was clear discoloration showing a high heat situation which means there were oil supply issues. Other than that there's no thread with any definitive proof of rod bolt failure. I'm not saying they aren't a weak link but if they are it's a pretty well kept secret on the internet. And we all know when something fails, no one ever complains about it on the internet.
In my research related to mechanical over rev, the consensus seems to be that the top end is the concern more so than the bottom end. Most indicate that the top end is the "sacrificial lamb" that takes the brunt of the damage. Many have just done the top end, cleaned the pistons and knocked down any dimples on the pistons and called it a day. That's where I was at originally since my leak down numbers on the three cylinders that didn't have bent valves were in the 5% or less range, there were no new engine noises that would indicate an issue on the lower end, and oil pressure was still good. First thing I looked at after the over rev was the oil pressure.
I guess what I'm saying is, I'm not going to let "while I'm in there" dictate how I proceed. I'll inspect things as best I can and determine how I'm going to go forward from there.
One thing I'll definitely look at if/when I choose to pull the rod bolts is the current stretch. I think it will be interesting to see just where they are. That might be the biggest reason for me changing them, to confirm after an over rev that they stretched. I'm not sure I'll be able to find the info to determine how much they stretched but I'm going to do some looking.
Again, I appreciate all the input.