The engine bay bolts and bottom of the fender bolts control the door gap. You have to manhandle the fender into position then tighten these down. Then use the two bolts behind the door tocontrol how well the fender follows the contour of the door.
On my car I had to change teh passenger fender because the car was in an accidnet and the fender was toast. The two months behind the door were bent slightly giving me a huge door gap. I just removed the fender to bend these and put it back together and it went OK. Takes a little time and a lot of thinking and you will get a good result.