IIRC, The '68 heads have a larger combustion chamber than the earlier 289 heads. Somebody should verify this, also there is a web site that has the info about Ford heads with all the specs. But I can't think of the site right now. Sorry.
The 65s defeintely have a smaller combustion chamber. Which means if you have say....a 1978 302 with 8.5:1 compression, if you swap the 65 heads on instead of the 68 heads, you will get a greater jump in compression.
Thanks for the feedback. I'm trying to find viton positive style stem seals for my '65, and I saw a listing for '68's. I wondered if the guide sizes were the same? I need them for .556 OD guides with the 11/32 stems.
65's had slotted valve guides and (stronger) cast rockers, whereas 68 has round valve guides and stamped steel rail-type rockers. The 68s also had a little poorer breathing due to a bulge in the intake runners from the smog air ports. 68's had larger chambers and are lower compession. Either is identical as far as intake, exhaust, and cooling channels and either should bolt up on the same engine. Don't mix them, however, or you will have a hard time with pinging if you ask any power out of them.