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maybe you switched the bolt with a shorter one somewhere, but you should be ABLE to use a spacer/few washers or whatever there if you can't figure anything else out.
stack washers or find a metal spacer at a hardware store. I had to do that with the aftermarket KG secondary rail... I was not impressed with fitment at all.
the blot doesnt have any thread on the top which makes me think a spacer is needed.
not always true, but it's possible. how long is the smooth shank? measure that then compare with the thickness of the bracket and, if the threads on the manifold don't start immediately, measure the depth there, too.
like I said, you very well might have mixed up bolts. I don't think the injector rail brackets are supposed to need spacers. did you remove these before now, when you're reinstalling, or is this the first time messing with these?