[cnavarro]

I was thinking the same thing as John, what is the exact cylinder height... they may have been a little tall, taller than what was used to set the compression height and hence the effective deck on your JE's.

If you do decide to shorten the cylinders, say by machining the deck that seals against the case, the real difficulty is without the proper tooling you'll end up with probably .0005-.001" variation in head to deck length of the cylinder measuring at say 45, 135, 225 and 315 degrees, meaning the bore won't be perpendicular to the deck anymore and there is also a chance that the cylinder tops won't be parallel to the cylinder bases.

It sure would be easier to blame it on JE or the rods though! Just check them out and ask more questions. Your going in the right direction.