First you must remove the existing dowels.  Then come up with two alignment fixtures that are .0015” to .0020” larger than the cam journals.  I call these fixtures “spuds”.

I rooted through my junk box and found an old wrist pin (I believe its from a mopar 318).  The wrist pin is .9843” diameter (.0014” larger than my RH cam journal, good enough).  That was pure luck.  I didn’t have to make a special alignment spud for the RH cam bearing.

I found a small piece of bronze stock that was large enough to make a spud for the LH cam bearing.  I machined that to .7877” (.0015” larger than my LH cam journal).  Ready to rock & roll.

Here’s what the alignment spuds look like.

Then put the head cover in place, shift it right or left to bring the upper & lower faces of the hole in the RH side flush, and tighten down the hardware.  You should not be able to turn the RH spud, the joint should close fully, and the faces of the cover and head in way of the large hole on the RH side should be reasonably flush.  If you can turn the spud, you need a slightly larger spud (maybe .0005” to .0010” larger).

Now that the head cover is installed and locked down in correct alignment with the head, drill and ream new dowel holes.

I chose the holes marked “A” & “B” on this sketch.

Here’s what hole “B” looks like.

I’m a lazy sort of guy.  I try to avoid machining parts if I can buy something that will work OK.  A quick trip to the local hardware store was in order.  I managed to find some bronze bushings with a .3755” OD.  They looked like they would probably work, and if they were too tight, I could always buzz them down a bit with some 320 wet & dry.  They fit perfectly.  A light drive fit.  A testament to how sloppy my old jalopy 3-in-1 machine is getting.  Can’t even ream a hole to proper size.  Any accurately sized sleeve or bushing will do.  You want a dowel ½” long with a .3750” to .3755” OD and a .250” ID.  Cut off two chunks ½” long and apply a slight chamfer on each end.  Then install the dowels in the head at locations “A” & “B”.  You want a light drive or push fit with no play.

Here’s a shot of one of the bronze bushings and a finished dowel.

Install the cam & cover along with a little assembly lube on the cam journals.  With the hardware tight, the cam should rotate freely.  Mine was like a greased pig.  Not even a hint of binding.

You could probably leave out the existing large dowel located in the oil feed hole, but there’s risk of the O-ring getting into the feed hole.  The dowel captures the O-ring and helps to keep it in place.  If you reinstall the old dowel as-is, it will prevent the head cover from being installed because the two new dowels position the cover in a new location.  Reduce the top half of the existing dowel to .412” diameter.  That way, it still has a drive fit into the cylinder head but has lots of clearance with the hole in the head cover, which allows the cover to fit nicely over the new dowels.  You don’t want to go much less than .412” and risk the dowel migrating up into the .390” hole in the cover, which would cut off oil to the cam bearings.

Drilling and reaming the hole at location “B” results in the loss of about 6 internal threads.  I used a 6mm x 1mm tap to cut two additional threads.  A longer bolt will be required to take advantage of those two new threads.  Tightening this bolt will be a delicate task and you will need to remain aware of the lack of full thread engagement.  But going easy on the torque at hole “B” should not present any major problems.  You just have to pay attention to it.  If you yank the threads out, drill straight through and install a nut on the underside, adjacent to the intake manifold.

I know my choice of bronze dowels isn’t the best.  Really should be steel.  But as I said, I’m basically lazy.  This is not a component that gets removed and replaced often.  The bronze should serve well.

This realignment process has worked out pretty well……so far.  The proof is always in the pudding.  I’ll have to run the assembly on an engine to be positive that the operation was a success.  For now, the future looks bright.

Yep........every time I see an eBay seller who has split the matched set and is selling the cylinder head cover separate from the cylinder head - I want to email them a good scolding.

Good job reconciling the irreconcilable differences!

Wow!
Thanks for documenting all your hard work.
Since the head and cover are line bored together, along with side to side misalignment when swapping covers, there is also a chance of a change in up and down clearance. Too much and the cam will wiggle, too little and oiling disappears. I know you said the cam spins freely, but it might be worth a look.
Perhaps use some Plasti-Gauge and measure the up and down clearance of the cam in the journal?
I've had some grief with mix-and match heads and cam caps, as well as heads and covers in the past. PITA, to be sure.
I could bore you with some stories...