I had to take off the whole front end of my car to fix the cowl, now i am having trouble realligning the hood to the fenders to the doors. Any tips?

 

Patience!!! Assuming that the gaps at the rear of the door are ok, start at the gaps at the forward edge of the door while at the same time getting the gaps right along the hood. It is not really hard, it just requires lots and lots of patience, fitting and refitting.... changes here require changes there....

 

+1. If you didn't actually reweld the cowl area and change any dimensional characteristics, then it's just a matter of fitting and refitting. It can be a tedious process.

 

This is what you need. It comes from the 66 (or 65, I can't remember which one I copied it from) Mustang(and other Fords) Service Manual. Get a copy.
Jim

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i hope you had the car level on jackstands