Even the new 'plastic' cars don't fit the best. I have had to cut up a door to make it fit properly on mine. There is only about 5/8 inch all around the door for the weather seal so getting the door in the opening can be a problem. My guess is that the body was cut up and not supported properly and the door opening was distorted. You are just going to have to start somewhere and this would be a good place. Keep focused on an area untill finished and you will gradually make progress. I'd surely try to get the body squared up before going too far. Even add some temporary supports to hold it there.

It looks like your car was modified to be a gasser at one time as were most of the steel cars. I can see a problem with the firewall and toe board. There is not much foot room in these cars and with your toeboard, firewall and trans tunnel pushed back you are going to have the seat very far to the rear. This will severely blind your view out the sides. Try adding a crate seat and steering wheel and you will see what I mean. I would really consider re-doing this as a 2nd project. You can buy a plastic dash if you want to save some work.

The motors were set back 10% of the wheelbase back in the gasser days according to the gas class rules. This is why there is the big relief in the firewall. There was also a crankshaft above the ground rule but I don't remember the number. It's also possible that the body was shifted to the right side an inch or so. This was one of the so called 'cheater' modification done. Logical measuring points were reworked to hide this. It caused about 50 pounds of load to be transfered to the right side.

Here is where to buy replacement parts.....be sitting down when looking at the prices. It's the only place I can find for headlights, tail lights and misc hardware.

http://www.willysreplacementparts.com/

Anyway have fun on the project. I'll be glad to help but I'm not the world expert on 41 Willys but I have been in every nook and cranny of my plastic car and done it all myself.