I have a similar issue with the hood on my '71, and I believe it's because the hinges are worn out, or at least one of the pivot points, allowing the hood to kick up I the back.
With regards to the door to fender clearance issue, I believe you will have to loosen the fender and pull it forward somehow (small bottle jack pushing the core support forward might do it) the hinge pillars (cab side) allow up and down movement the door side of the hinge allows in and outward adjustments.
So, that being said,I think loosening the fenders and pulling/pushing them forward might do the trick.
Ben
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"Persistence is the twin sister of Excellence.one is a matter of quality,the other, a matter of time"
“Serious Black” my 1971 Short Bed Fleetside Sold to
an outstanding man in Lees Summit,Mo. “Gone, but by no means,Forgotten”