I know of no engine where the pistons at TDC are higher than top of the barrel. Always been flush and seldom a few mm lower. If they were higher they could and would smack the cylinder head, especially if oversize after a rebore. Sounds like the con-rods are not original spec or someone has skimmed the top of the barrel. Put a number of cylinder base gaskets below the barrel to lift the barrel up a few mm.