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I picked up a set of these as the ones I have are showing some signs of wear (in particular, a bit of side-to-side play in the first value) but on the new ones the "stub" that goes into the slot is a bit too long. What is a good way to shorten them so that they fit properly but does compromise either the guide or the valve casing itself?

I don't think the original tooling has survived and has been replaced by new molds. There could be some very slight variation and trimming a bit off the bottom of the part that fits down into the slot in the top of the piston should not compromise function or durability.