Oh BOY!
I have a pit in my stomach just looking at that.
Its okay, its not ruined quite yet.
Follow what tripper said. Your gonna need to get some jacks. Screw jacks work best for working horizontal. You'll need to spread the door jambs till the hinge side looks good. Once the hinge side is good and square with the floor, run a diagonal brace from up high near the windshield to the floor. That will lock the front half in. Throw in a few, one near the doors and one in the center. THEN, use the doors to line up the reveal on the latch side. If you can get the doors to work well, your set!
Bracing is a must! I just used rebar to brace mine and it worked okay.
Once you start putting your top on, learn from my mistakes and only tack everything together! I went and welded 1 section fully and have been fighting that section since!
TAKE your TIME! Its important since if this part doesn't make you happy, you'll hate the entire build. Then your chances for finishing will be slim to none.
Be careful when welding all your sheet metal together, you dont want to just blast away. It'll get too hot and warp all over the place.
I think with my 7" shop, i had 18 separate pieces when it was all said and said and done.
Don't get discouraged just yet.
OH, and also, before you weld the whole roof in, take a break away from it for a couple days, then come back and look at it with a fresh mind. I wish i woulda done that. I would have taken another inch or 2 out of the front. Now its just too much work and i have a slight "nose up" look to it :/
Heres a couple photos of mine