Had the same issue, doors were misaligned and would clunk when shut (or even not close if car is parked on a curb without lifting the door up). I did exacly what karlj said, didnt use a jack though. No need to be honest. Just open the window, lossen the bolts, get you shoulder into the window and lift the door, with the other hand tighten the bolts. Just dont go too far or the door would be too high and still clunk, if it does just repeat the steps only this time lowering the door.
Hope this helps, unfortunately previous owner didnt bother fixing this so now the bottom of my passanger door is a bit scratched up on the inside.