Is the alignment problem that you have in the gaps at the door/fender, or is it the top of the fender not being even with the door? If it is the gap, it may be adjustable with shims. How was the alignment when the vehicle was disassembled? Maybe it is a problem with the fender not being OEM.
Bad body mounts can cause problems with alignment of panels. If the body lines line up and the top is not even, it is not likely a problem from the mounts.