The 2S cam has a higher lift than the stock cam. When installing an Atlas cylinder on my 1972 Combat, the 2S camshaft lobes hit the bottom of the tappet bores, just as you were describing. It was a simple matter to remove a small amount of material from the bottom of the tappet bores. It does not need to be done precisely. I may have used my mill, but it easily be done with a hand held grinder.
You may want to add a couple more possibilities as to why your engine displays contact marks.
E). Assuming the original cases, cylinder, and cam, inadequate clearances were machined at the factory.
F). The cases, cylinder, or cam were changed later and the tappet bores were not machined.
Meanwhile, back in the real world, it probably doesn't matter. Get out the grinder. It's a 5 minute job.
Agreed, a simple fix.. Already done months ago. I am just one of those that like to get to the bottom of such things.
FWIW, I put like 25000 miles on this bike in 3 years time back in the late 70s. I only discovered this issue while inspecting the parts recently.
I could find no documentation or discussion on this even being a possibility back in August when I first discovered the issue.
I relieved the interference in mid August using the original factory 2S cam as a guide to how much to remove. Used hand held rotary tools. I have no lathes, mills or any sort of such machinery. Hell, I don't have so much as a compressor or drill press!
In late September when I acquired a replacement 2S Hepolite branded cam I again had clearance issues. Hand to remove more material.
All discussed on my "ressurection" thread.
At this point I have no doubts whatsoever that cases, barrels, etc are original factory and this engine left the factory with this manufacturing defect and another I will talk about later in a separate posting.
The reason for this separate posting was that it had been asked if the cases had been 'decked'. This is the only engine I have seen so I have not the experience to tell by looking at it. I sought a definitive means of determining if a set of cases had been decked or not.