I've never heard of 9 bolt heads cracking or issues with cracking. 8 bolts heads yes, but not 9 bolt.
You are correct, a 1968 TR6 should have a 9 bolt top end with cast iron cylinder barrels and aluminum single carb head. Since you say your bike has an 8 bolt top end with cast iron head it would be interesting to see what you have since what you have seem to be Pre-Unit items, at least your top end anyway.
But, if you don't care so much about originality, assuming it is in fact a '68 TR6, then the top end you have now if it is running and good at that, you might want to leave it that way....at least until it needs a rebuild. Shouldn't be any cracking issues with the cast iron cylinder head either...only the aluminum 8 bolt heads.