I have a 6.9 I have had since virtually new. At about 250,000 a lifter roller failed and took out the cam. The head gaskets were weeping so I pulled it and did rings bearings cam and rebuilt heads including surfacing. I don’t recall having any issues installing the intake manifold.
At 500,000 it really beginning to go through a lot of oil. I should have replaced the pistons the first time because ring groove wear was the problem. It was kind of a pride thing “look at that 250k and the pistons and cylinder walls are fine”
So it got rebuilt again, the heads needed surfaced again as well as the block. The heads are down to the minimum thickness. No valve protrusion issues because it was a HD diesel experienced shop. They sunk the valves in to match.
The point of all this info?
When I went to put the intake manifold on I had to drill out the holes to get the bolts in.
Wether it was a tolerance stack up, different gasket thickness or what I don’t know but it turned out fine.