What is the best way to replace door hinge bushings on a 69 A body. Upper hinge.

For the smaller upper hinge that came with factory bushings, simply tap out the old bushings and tap in new bushings with a new pin.

The larger lower hinges that had no factory bushings should only be rebuilt by drilling and reaming and installing an oversized pin, not by installing bushings where there weren't any. Here's a link to a good kit. Don't buy kits that include bushings for lower hinges.

Do the hinges only bolt on one way or is there adjustment in the hinges?

The hindge itself doesn't have an adjustment. The adjustment is the cowl holes are oversized, squared off. That's how you adjust them. Same for door side of hindge.

Thanks, that's what I was asking, if there was adjustment in the bolt holes.