The end of the pillar post should be even at the bottom with the filler strips. When you say your doors are out at the top tells me your hinge pillar is too deep into the sill. If your sill was also rotted it would be very easy to get the arc of the lower body line off enough to get you that problem. You need to correct that now or it will just keep compounding issues as you go.
In the first picture is my 32' Olds roadster body, all re-wooded and ready to start prepping for painting. In the second picture is the only Olds roadster currently being campaigned and shown. If you look at the picture of my Olds body you'll notice the long slow curve of the body's lower line. Your 32' 4 dr will actually or should have that same sort of long graceful curve to it. Because I'm restoring my Olds, I went to the Olds national show hoping to see one or two 32's. I didn't expect to see this roadster but it was there and was perfect for me to take some reference pictures of. When I was taking pictures of the car, at the time, I couldn't put my finger on it, but I realized something didn't look quite right on the passenger side. Talking with the owner he told me much of the wood was totally missing and they had to reconstruct a lot of the car. Later, looking at the pictures I realized what had happened. The lower body curve had been lost in the restoration and they had mistakenly straightened the body line out. By doing this on the bottom, it compounded things further up and made it necessary to do some incorrect things to try and correct the problem. I won't point out the obvious but I'm sure you'll see what I mean. I hope no one runs and tells the owner, if they know him, what I posted here, as I'm just trying to show why it's important to correct any issue in your wood framing before going any further in your restoration.