Chainbox spacers?
 

After a case face and alignbore is it possible to make the case too narrow so that the chain boxes need to be spaced out (like cylinder copper base gaskets)? That way the cam locking plate is centered over the cam?

Depending on the thickness you need, there are options:
There is a .020", .030", .040" paper and the 964 aluminum spacer/gasket also .040".
If you need to, you can stack one thin paper with one aluminum gasket.
If you need more than .050", cam centering is the least of your worries.

Thank you Henry

I just reread your post. Are you saying the case was trimmed (presumably to align bore back to standard) altering the cylinder stack. When the stack was shimmed to create the proper piston deck, the chain boxes no longer aligned with the cams.
I'm wondering why the machine shop that did the work didn't send chain box shims with the case?
How much material are we talking about?

No machining done yet. Just planning ahead.

In that case, no, you won't need to trim the chain boxes. When the case it trued up, only a couple of thousandths are removed (hopefully) before its line bored.

The conversation is not about trimming the chain boxes. When the case is decked (I believe more than a couple of thousandths if the purpose is to rejuvenate the mag case mating surface) there starts to be some compound dimensional issues. Case decked, chain box mounting surface to crank center is reduced by the same amount. That dimension must be recovered.
Same with the cylinder spigot. Barrel spacers (base gasket) are definitely required. Now, "how do we shim the chain boxes?" is the question.
I listed the shims/gaskets available, I have had some custom steel shims made (for long rod engines) but my question is, why doesn't the machine shop offer a shim that compensates for the machine work? Maybe they do, I just don't have the answer.

So machinist thinks case needs .25mm (worst case .5) taken total from case haves. That’s about .010” or .005” per side so. I guess I’ll mock up the build with the thicker paper gaskets, take some measurements and get back to you in a few months when the machining is done.

If I understand the OP's issue, the cam nose isn't centered in the cam box because of the machining of case, cylinders, heads, etc. to reduce the stack height. That should bring the cam axis closer to the crank axis.

Depending on the amount removed from the "stack", trimming the chain box housing mounting surface should re-center the cam. However, the chain may now be too long. Too long for the adjustment range of the chain tensioner.

This was the case of a previous engine transplant. Years ago, I purchased a rebuilt '69S long block and upon inspection, the cam wasn't centered in the chain box. I had the chain boxes trimmed according, but the chain was also too long.

At the time, I hadn't considered spacing the stack under the cylinders, etc. But maybe I did and didn't want to further reduce the anemic compression ratio as a result of using factory RS pistons (6.5:1 actual CR with the 2 liter crank), or I was at a build point long past installing cylinder spacers.

Anderson's Performance Handbook mentioned oversize chain idler sprockets to bring the excess chain slack within tensioner range, so I sourced a pair from German Precision (Santa Clara, CA), but again, this was years ago.

FWIW

911cars and dannobee, when the case mate faces are machined ~.5mm, .25mm and then the mains machined to standard, the case is now .01” or .02” narrower. Copper cylinder base gaskets can add this back And needed to set the piston / cylinder clearance. This puts the cam nose back to the stock location. However the mounting points for the chain boxes are now narrower. The bore for the cam lock plate in the chain box and the cam nose are not concentric anymore. A spacer is needed under the chain box to restore the material lost. I hope when I do the dry assembly I can get the .005” or .01” thicker chain box gaskets from Henry or pelican....

Agree, but what if the cylinder heights are trimmed to make them identical? What if material was taken off the cylinder heads? The cam axis now sits closer to the crank axis. If so, the stack height is now reduced by the amount removed. To re-center the cam inside the chainbox oil seal, a like amount of material must be removed from the chain box mounting surface.

Sherwood

Back in the day, most engine builders discovered that Porsche spec pistons were advertised with greater compression than actually measured. Mahle was locked into a minimum volume for custom pistons and aftermarket companies lacked the expertise to forge a viable option.
Shortening the stack on a 911 engine was a last ditch effort to milk compression from pistons lacking dome volume. "ask me how I know"
We went as far as shortening the cylinders .080", machine the piston domes and using half-links in the timing chains.
In today's world, there are plenty of reasons to lengthen the stack but zero reasons (sans budget) to run with compromised/shortened dimensions.

Most of my concerns with the OP hover around the amount removed from the case.
Although I understand the concept (flattening the case halves to improve main bores and outer sealing surfaces) I question how important dimensions like intermediate shaft and distributor drive gear back-lash are recovered.

Intermediate Shaft Dimensions 911SC
 

I am looking for the intermediate shaft dimensions. I can't find in the Porsche Manual, my guess is that since the manuals build or augment new data as the years rolled by. It looks to me that the shaft hasn't changed in that bearing area since the bearing application goes back to 1966.

Background: There is brass showing on the old bearings both forward and aft, and the thrust surface.