Been a little while since I posted, so this'll be a longer summary.
Following up on checking the intake manifold template, I put my mockup block with actual cylinder heads on a mill and went to town. I eyeballed it square, then used a gauge pin in the end holes on the manifold bolt patterns to properly square it up in the mill.
There are two steps that have to happen to modify the heads for the later manifold. The first is modifying the flanges so the manifold will drop in place. The second is drilling the alternate mounting holes so the manifold will bolt down. I had all that figured out in the template and had to do it all in this one setup on the mill. The width of the space in which work was to be done was winder than the Y-axis travel of the mill table, so I had to slide the head in/out to get everything. Because of that I had to do everything on the right bank first, then everything on the left bank.
In starting on the hole pattern, one of the first things that becomes obvious is that the flywheel end intake ports are over top of water jacket passages out of the heads to the waterpump. This means you can't drill indiscriminately into/through things.
This is a photo into that port. The bulge down from the top is the boss for the original manifold bolt hole.
While cogitating on how to deal with that, I went ahead and scalloped the flanges.
Of course, once I put the effort into scalloping the flanges, it became fairly obvious that I should have just buzzed down the entire row instead of carefully sculpting them.
Moving on to the manifold pattern, I was able to drill most of the holes uneventfully. Only two needed to be counterbored because they ended up on the edge of a sloped surface.
I had to very carefully control the depth of the one over top of the water jacket passage, but there's enough of a boss behind the original boss that I was able to drill a usefully deep, although depth-limited hole at that location.
Where there aren't cooling jackets under the flanges, there's actually free space. Most of the holes drilled straight through, which would make tapping them easy. I didn't tap them this time around, though. One of the holes ended up with a surface below the flange halfway through the diameter of the hole. The drill walked and wobbled the hole before I realized it. I was very careful about drilling the other hole affected by this issue after that.
Even with all of that work, the manifold doesn't quite sit down on the intake flanges.
As this point I graduated from planned/engineered mods to the fit/futz cycle.
I had to do some extra whittling... which I was fine with doing since this is my mockup block.
After these mods, the manifold finally sat on the intake flanges without running into anything. Unfortunately I flaked on grabbing a photo.
As I believe I noted in playing with the template, one of those things was to raise the port flanges by 1/4-3/8". That means the later manifold say lower in the V on the early heads than it did on the late heads. That's where the block interference came from. After I was able to get the manifold to have clearance everywhere and sit down on the flanges, I tried to fit check with the starter.
Note the gap between the manifold and the intake flanges.
Of course, GM changed a LOT of things in the intake port and flange configuration on the cylinder heads when they went to the later manifold.
Ooops. Not really anything reasonable to do about that. Back to the drawing board. At least now I understand what needs to be done for this, and I've discovered one more way that won't work. Look out, Edison.