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What I did with this same seal on someone's car is match the end parts that match the metal contours first, then find the center and fasten that part. Now work toward the ends and bunch up the two formed parts so that there's a couple troughs. Seemed to work.
Clearly there is primer still flashing off under the paint. Gases in the primer are causing the bubbles. Sucks.
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Maybe it was Gene's Ranchero. Gene, doesn't that look familiar? I tend to do some things on autopilot, so can't recall if it was yours.
[Edit] Never mind - I just read up top instead of just looking at the pictures (that autopilot thing kicking in) and see Gene already posted. Gene, I thought it would have been pretty good.