i want to align my doors and them dang bolts suck and i want to put some regular hex head bolts.

Also at the front of the doors is the door has dropped down some on the passenger side and i dont want to relocate the hinges. Can i just drill out the holes on the hinges and make the holes bigger

 

The screws going into the doors are M8-1.25, 35 or 40m/m long should give you some working room.

The body side of the hinge is welded to the pillar, not screwed into a plate. To make it a bit more adjustable, you'd have to cut the hinge off, cut/drill/tap a repair plate, and the put the plate in while you screw the hinge to it. That will buy you some movement.

If the hinge is misaligning, the weldments may be cracking - strip, prop up the door, and re-weld.