Interesting, you took a slightly different approach than me. Thank you for the info. The weird thing is that with my mod of replacing that bolt with a shorter one, I can move the saddle all the way back. So even further than yours. And the intonation is still slightly off. And my D saddle is way further back than any of the others. Hmm.
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That is weird. Maybe ask for a replacement D string from Pyramid or the distributor. I want to put the Pyramids back on to double check but I think they intonated very close to the LTF pictured above, maybe a little forward.