I was recently told the only difference between the 5 and 6 was the roller cam/longer cam bores and an insignificant change to the timing cover. The cooling passages did not change. Just a guess but I think people assume there were problems with the Gen V because it wasn't here long, yet no one really cites specific issues they've experienced. So far, the only really factual explanation I've unearthed is they made the change to accommodate the roller cam.

BBC Heads
 

There is a HUGE difference in the coolant passages on the deck of the Gen V block -vs- the Gen VI block. While they were "fixing" the head gasket/deck problems, GM changed the timing cover bolt patern (The oil pan/front seal location was already changed in Gen V) changed cam snout sizes (affecting timing chain sets) and thickened the lifter galley in the block requiring taller lifters or the use of Gen VI roller lifters. They also took away the mechanical fuel pump provisions.

There are also early and late Gen V's. (Some have roller lifter provisions and mechanical fuel pump mounts and others do not.)

To make things more confusing... Bow tie Gen V blocks do not have these changes and have conventional coolant passages.

Curtis @ Bilet Marine

bigblock gmc heads
 

i havent had any head gasket problems.......but,i think i would have.i say this because on the deck of the block ,on both sides at the bottom of the deck,towards the exhaust side there was erosion about 1-2 inches.it looks like the gasket was going away.

I've looked at the two side-by side and see no difference in the cooling passages. Obviously they're quite different than the Mk $ but the V and VI even share the same gasket.

What am I missing?

The Merlin heads wil work just fine on that engine. Their flow numbers are a little better than stock heads but not enough to cause any problems. Port locations are the same as stock heads so no problems getting the exhaust to line up. Plus if you have them, no expence and maybe a small increase in performance.

I managed to locate a copy of the HP Books Rebuilding the Gen V and VI big block- there are lots of subtle differences between the two to increase reliability and possibly cut manufacturing costs. PS- that book is out of print - I had to get mine from the U.K. to avoid paying $100+ from the rare book people.