Go get a can of white lithium grease (not WD40, that'll only temporarily fix the problem until it evaporates) from a home improvement store like lowes or home depot. Squirt some on the hinges using that little straw that comes with it (unless you want a big mess). Once done, move the door back and forth a few times, allowing it to work it's way into the hinge. If it's still making that "popping" noise, shoot some on the bottom hinge on the top of it where that contoured metal piece has the roller sliding on it as you're using the door (sorry for the horrible description of that, hope you got what I meant). You're problem should be fixed.
I had the exact same thing happen, only it was my passenger side after I replaced the lower hinges. I had this god awful scraping noise and my door refused to close unless I pushed on it kinda hard. Not sure if you rebuilt or replaced your lowers, but take a look at that top part of the bottom hinge that's contoured. Compare the old with the new. You should find that the new one has defined round parts with a point in the middle, and on the old hinge that's more than likely rounded off. Your scraping noise is coming from that roller I mentioned having a hard time "rolling over" that point so it sounds like metal scraping metal. A little grease there lubricates it and helps it slide over the point easier. Mine have had no issues since, and operate silently.
Sorry for the long post, hope it helped.
__________________ 2003 V-6 - the usual bolt-ons. Gremlin taking up residence in the idler pulley. I'll finish this one when I'm done with the other one.
1965 coupe - Born - straight six standard issue
Now - 5.0 motor, T5 tranny, R&P, full length subframe connectors, draglink bars, hedman headers
Coming soon - disc brakes, electronic ignition and a whole host of other stuff I forgot to mention. The list goes on and on. Basically, it's my new toy  | 
