Installing goodmark door skins and quaters on 66 chevelle and body lines will not line up. I think door skins are bad. Goodmark rep has not heard of any problems. Any help would be great.

Are your hinges good?,check the bushings.If you removed the quarters and the car was not fixed/stable it might of moved.Is the trunk pan in?Sometimes the car needs to be braced if removing a lot of stuff.Was the car on jackstands when you cut the parts out or on the ground,if on jackstands it may bend.I made wood tables that the car sits on which raises it about a foot and a half with the tires,which will keep it high enough to work on .I did a few convertables ,did the same and also braced the car as well.Some guys will take a car rim with a pipe welded into it,then tack weld the pipe to the car once they have it level so there is no movement when cutting and then welding.I always use clecos or sheet metal screw to get the quarters on.A couple in the door jambs,some in the trunk gutter .I try to have the trunk on for alignment purposes also.As far as the skins go I have my own method that my dad taught me.I like to have the fenders on radiator support so I can line everything up.I try to get 3/16 gap or as close between all the body panels.I always ground the skins off lightly crimped the door skins on,put the door back on and checked for alignment and make adjustments.Once I like what I have I tighten the crimp. with the door on the car.I then remove the door close the crimp.I tack weld the skin on .Some guys use panel adhesive.and dont agree with my method. I like to do one side of the car at a time making sure the hood lines up with the fenders,fenders with doors,doors with quarters and quarters with trunk.It has always worked for me.There are lots of different methods of installing body parts.Goodmark parts are pretty decent but not always perfect.Take your time and dont do your final welding until you are 100% satisfied with the panel alignments.I would have every body panel on the car on and fit up before I start to weld.Jump around making small tacks until you connect them all.It is time consuming but it will show on the final project.Good Luck.Post some picture if you can .Lots of talant on this site.

I totally agree with the above, testfit, testfit, testfit! If possible I always try to rebuild the hinges so the pins are removable, then I fit the doorshell frame to the rocker/quarter/fender and pull the pins and remove the door. I install the skins but do not weld then reinstall the door and adjust as necessary for as close to perfect fit as possible then carefully pull the pins again and remove the door and weld. If you work the skin on slow and hold the dolly just right (not completely flat against the skin) and use the right shaped hammers for the shape of the skin you'll have very little to no distortion folding that skin on. Take your time and testfit it well.

Did you cut off both the skin and 1/4 at the same time? If so it would be wise for future refernece to remove one panel at a time.
I would remove the door skin first and use the fender and old 1/4 panel to algin the new door skin. Once the door skin fits and is installed THEN remove the 1/4 panel.

If both panels have been cut off then its a matter of adjustment til they fit right.

With a skin off the door, that frame will bend and move to any shape you want it, so now is the time to correct any fitment problems.

A small step by step on doing door skins.
http://rides.webshots.com/album/561536276SkBsQw

I have hung many Goodmark qtrs and the top style line on the A/M qtr does line up with a original door skin but does not line up with the A/M door skin it was alot of work but thats all you get, good luck.