My 340 in my 66 developed issues :-(

How do you guys feel about .060 over? Right now it's .040 but I discovered
Something I don't like and am pulling the lwr end apart tonight. I noticed for one, that the right and left banks have different Pistons installed. And also, there is quite a lot of wear at tdc in the cylinders. I would just feel better doing the whole engine rather then putting a fresh top end on a mystery lower end..
I just am unsure about the .060 over part!