snow guy, the doors and front fenders have some adjustment thru the mounting bolts which have slotted holes to help with alignment as well as small metal shims. Start with the doors first, lining them up with the B-pillar or back of the cab. The striker can be moved by loosening it as well. Move the doors by loosening the hinges. The hood is adjusted thru the side hinges, either on the hood itself or the fenders where they mount. Basically, anywhere the body panels attach will have some adjustment. Just go in small steps and only loosen the bolts enough to bump the panel. I use a small sliver of wood, like a paint stick, to keep the body lines even along a seam.
If you're going to remove any parts to paint them, like the hood or fenres, drill a small 1/8" hole thru a spot where you can re-align the panels after painting. A good area is where you have a tab and a bolt thru it, like the top of the fenders inside the engine bay, JSM84