I would like to see a thread EXACTLY outlining the differences, and ID, between the MK4, MK5 and MK6 blocks and what will/will not interchange.
I believe that I know most of the differences,, they are not that complex and mysterious. The later blocks are termed Gen 5 and Gen 6, and the earlier ones MK IV.
Besides casting numbers,, the Gen 5 used a 10 bolt timing cover, similar to the MK IV timing cover, but they are not interchangeable, due to differences in the oil pan. Gen 5 and 6 pans are the same, the MK IV different. The Gen 6 timing cover is a 6 bolt cover. I believe there may have been some crossover blocks between Gen 5 and 6 that didn't have the "proper" number of timing cover bolt holes.
The Gen 5 block has different water passages in the deck surface, and causes a sealing issue if you don't use Gen 5/6 style heads (including GM bowtie). My understanding is that is one of the key reasons the Gen 6 block was developed, to allow aftermarket and MK IV cylinder heads to seal the water passages properly. The cylinder head bolt pattern has remained the same for all three series of blocks.
Gent 5 and Gen 6 blocks use a camshaft with a stepped nose, and therefore a different timing set. The step allowed the use of a camshaft retaining plate to control thrust. A MK IV style camshaft will fit into the block no problem, but requires the MK IV style timing set.
Gen 5 and Gen 6 were the first of the factory roller cams, as far as I know, although there were some flat tappet cams in some of the Gen 5 I think. The Gen 5/6 rollers use a new style roller lifter that requires the "dogbone" type stablilizers to hold the roller in line with the cam, and then a sheet metal "spider" that bolts into the valley to retain the 8 dogbones.
The factory Gen5/6 cylinder heads are not set up for valve adjustment, they have rocker bolts instead of studs that retain the rocker arms, so for a performance application, the bolts should be changed to studs to allow for deviations in valve train geometry from factory pushrods and cams, or if you want to run a mechanical cam instead of hydraulic.
Gen 5/6 harmonic balancers and flywheels/flexplates have a different counter weight, and of course the crankshafts are of the one piece rear main seal variety. You can purchase a two piece rear main seal adapter and run a MK IV crankshaft in a Gen 5/6 block.
One of the less obvious, but more important changes in the Gen 5/6 block is the oiling system. It's considered a "priority main" oiling system, and is the same basic oiling system in the aftermarket blocks like Dart. For long time users of the MK IV blocks, it's especially important to understand the two pressure bypass system in the newer blocks, one of which diverts oil to the oil cooler outlet and inlet cast into the block in front of the oil filter location.
Another thing with the newer blocks is that GM recommended a maximum over bore of .060". I have done some visual inspection of some of the blocks, but have not paid to have any sonic tested for wall thickness, so would have to say they have a reason for suggesting that limit.
Most of the Gen 5/6 blocks lack provision for a mechanical fuel pump, but I think the tall deck (or truck block) still have it, as well as the Bowtie and also the HO 454 crate engines.
Might have left out something,, but time for something for dinner!