[bouncytruck]

My hard top isn't on the truck, so I don't have any pics, but it goes on the underside of the door glass frame to the underside of the windshield frame. They have about a 45 degree bend in them so the wide part can mount to the hardtop and the narrow part mounts to the windshield frame. Look and see if you have two holes in each spot, which is where it screws in.

Also, find yourself a tube of RTV or weatherstrip adhesive. Put a few spots on the bottom of the header seal just before you put the top on the windshield frame. Sometimes, driving around the block with the top loosely bolted can help settle it in place a bit more.

For the gaps around the doors, are they at the top rear corner of the door? If so, I'd still suspect the body mounts. You may need to shim them a bit to raise the center of the body.