in order to get the alignment of the doors near perfect you have to take the fender off.
the door has a huge range of adjustment and can drive you nuts.
Its really hard to get your hand behind the fender to properly access the hinge to body bolts.
plus if you replaced once hinge there is no guaranty that the upper one isn't worn out completely.
first i would recommend rebuilding both hinges with new bushings and pivots. if the new bottom hinge is from another car and used even more so. you want both hinges to be 100% before you try to realign the door.
remove the striker for the lock, you want to be able to open and close the door with out the lock for now.
put some masking tape on the door sill to try and protect it. and have a look at how rusty the bottom of your doors are around the seal area. (sometimes a hammer can help *fix this area to get things back in line.)
the bolts behind the fender will give you movement up, down, and allow you to raise or lower the back edge of the door.
the bolts on the front of the door allow rotation movement that swings the bottom of the door in and out from the rocker.
first you want to set the bolts that are behind the fender on the cowl. You will spend hours, getting the alignment just right. you will open and close the door about a billion times.
besides raising the tail of the door up to prevent it rubbing on the sill area you want to keep checking the alignment against the quarter panel all the way down and also the alignment of the ridge line that starts on the front of the quarter and goes across the middle of the door and onto the fenders.
Don't pay too much attention to any decals usually the alignment was crappy from the factory and then the decals were installed with bad body lines anyway, so ignore them they could be like 1/8" out of alignment once you get everything were you want it.
once you happy with the fitment of the door and alignement, close the door and roll up the window and check the fit of the window against the seal.
there is a good chance that any changes you made to the door will have put the window out of wack.
so pull off the door panel and make any changes you need to the window.
phew now its time to install the striker.
now the striker can help you gain a little bit of lift on the back edge of the door if you need it.
basically install the striker a little loose and keep opening and closing the door making adjustments you want the door to open and close easy, but you also want to hear the double click of the lock when its shut. you may find that you got the door to open and close smoothly and you can hear the double click but the door sticks out of the quarter panel just a little. move the the striker in just a hair and the door may be a little hard to close, but the rubber seal will relax a little over time and then the door will be fine.
its more art then science, our cars have horrible panel alignment and lots of corners were cut during production. i found my cars passenger side was all out of wack with factory panel alignment holes all misaligned and they tried to compensate by redrilling holes and moving things even more out of wack.