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What I do is use a small screwdriver and while the flange is out of the way I push on the side of the pipe so it goes into the exhaust port I don't really use the flange to pull the pipe into the head . Even if I have to wiggle the pipe some to get it to sit correctly . After its flush and seated I then slide the flange onto the studs then tighten them down .
I called fuelmoto on this very issue. I was told that when using HD tapered gaskets that there will not be much thread exposed after the nuts are torqued. (99 inch lbs is what fm recommends). Mine did not "click" into position either but they do not leak. My bike had 600 miles on it, I reused the oem gaskets, just left them in the head.
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