Thanks for the tips Mr Wizard. I will do a magnet test on the roof, I just assumed it was steel from the appearance. I'm on the fence right now about removing all the old sealant. The bondo stuff is very hard for the most part, and it covers the whole rail and join very well. I am thinking it is a more solid join than I would have with dicor and e tape. Maybe less (work) is more (effective) in this case.
I will look into the vibrating multi tool, but a heat gun and an 1 1/4" scraper wasn't too bad so far. I have about 12', bathroom vent, and 3 roof rack anchors cleared so far. I also have proflex, using proflex for the areas I've cleared with dicor smothered on top to "bulk" it up a bit to match the original before applying the e tape.
I'm not able to doing anything today, so I am sorting out my strategy.