With the help of Jeremy who is still in town working as a tech rep for Kelly Aerospace, I test fitted the cowl while the toplate and "banjo" of the FAB were in place. The alignment is good.
I also worked on fitting the cowl. I positioned the top cowl and added another cleco, this one to the top, making three total. I trimmed more material from the port side of the lower cowl, and the starboard side. I still have some trimming to do but it is making progress and looking pretty good.