You may have an epiphany about the cause of the problem, but I've found that slow and systematic really does work. First engine I rebuilt I put the main bearing caps on backwards. All of them. That engine sure felt tight.
Don't dis a flywheel bolt problem. I bought an engine from another Big Bolter, and it didn't look like it had ever been apart, although it did look like it had a lot of miles on it. I would be surprised if the flywheel bolts had more than 20 ft/lbs of torque on them. I'm surprised that didn't come apart before it left the factory.
It certainly isn't going to hurt to Plastigage the rod and main bearings, but I think that if the clearance has gotten large enough to make the engine knock, you would be able to see it.
I've recently dealt with ARP about fasteners for 235s. The engineer I talked to sent me a nice spreadsheet to fill in with every conceivable fastener specification required. What you need is interchange information. Is your rod bolt the same as was used in a 1964 Chevrolet 327? There are certainly lots of those around, for cheap. I wish I had the answer to that question, but I'm going to have to find out about mine the hard way. I'll post my findings if I don't die of old age before I finish the re-build.