The builder wasn't too great at drilling holes accurately
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I am wondering if the casting was a little off because the 3 holes at the top all line up near perfectly in relation one another if you lay a straight edge on your screen at the bottom of each hole. Or is that a camera created illusion?
The hole locations in the steam chest cover all seem quite acceptable. The only issue really is the top center stud is loose in its threads. The stud location is fine, it just droops a bit, so I suspect that hole was wallowed out a little when drilled, or perhaps it was originally started to be taped at an angle and needed to be re-taped at a different alignment. I'm not too worried about it, as it just needs to be lifted slightly when putting the cover on, and it cinches up fine. I think the old bit of copper wire trick will tighten it up just fine when I go for final reassembly.