you got a complete model and serial number of the truck this engine is in?
dumb question but i'm sure you have looked and made sure of the engine model by looking on the side of the block on the flat surface where they stamp the engine number? Maybe there are other numbers there indicating a special application or something?

I've looked through every engine manual cat has on their GP25 series trucks and they all show a standard 2 valve per cylinder setup. Nothing to indicate a 3rd valve.

This is rather odd setup,unique apparently and may not be factory OEM setup. I've worked for cat for years and never seen a 4G63 or 4G64 with this head setup you speak of.