Is the gap from the front fender to door correct or is it off as well? Because if the gap between the fender and door are correct, you will not be able to adjust the door properly. As you raise the rear of the door, the front gap will start to close at the top. Your mention of extensive work being done on the left side of the car got me to thinking. If the car was hit in the left door pillar area hard enough, it is possible that during the impact the rocker panel was pulled upward. If this wasn't corrected properly when the repairs were made, this could account for some of the odd fit. Just something to look into.

Chris