If you did NOT remove the hinges from the cowl side panel, you should be able to re-install the doors by laying a 1/8"strip of masonite on the door threshhold, direct the door into the hinges (install the bolts loosely but do not tighten) then close the door so that the bottom of the door sets on the strip of masonite. Use this as a starting point. If the door needs to be raised more, go inside the car with door closed and stick a wonder-bar between bottom of door and masonite and pry upward, then tighten bottom bolts. You can't access the top three bolts unless the door is open, so it is best to have a second person on outside open door while holding it up while you tighten top bolts. No need to go crazy torquing bolts down at this point. Several more fine tune adjustments may be needed.
Doors can be adjusted up, down, forward or backward. Use your wonder-bar to push the inner door structure (with bolts loosened) in the desired direction to get the most even fit all the way around.