The shims that gearjammer posted are a great option but if you dont use them it might simply be that everything is as you said: not lined up. Sometimes the custom brackets are shorter or longer slightly. Ive seen where some guys have to cut 1/4" off a bracket set or use washer to SHIM OUT the entire device to make it line up with the other items.
OR, its possible the AC is slanted? If its not straight it'll toss the belt. Most likely the older items should be left alone since the ac was added later. Its not an uncommon problem.
Dont look at the brackets for lining, look at the pulleys and belts.