I encountered a similar problem with my '53 Sq 4 MK II.. after head rebuild, I discovered that a couple of the collets were noticeably larger than the others, causing the valve tip to protrude higher than it should. With guidance from my US guru, Paul Ackerman, it was determined that I needed the later year spring caps and stepped collets..Those I was able to obtain from the UK Club spares inventory, and that solved the problem, now all stem tops are pretty well flush with the top of the valve spring hat.
Another related issue: I had one slightly bent pushrod, so ordered a replacement from Dragan for my year. After assembly, I couldn't get any clearance at all with the rocker. On closer inspection, it seems they sent me a later model pushrod that has a smaller diameter tulip cup, and so the rocker ball couldn't sit all the way down in the cup.
So many little things to go awry with these beasts.
Phil Auldridge Austin, Texas - USA
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53 SQ 4 MK II, '72 Norton Commando, '78 BMW R100/7, '79 Honda CBX, 2014 Indian Chief Vintage