To get the alternator to fit out of the engine bay, you must remove the mounting brackets for the alternator as well. Once you remove the brackets, the alternator will fit out of the bottom of the engine bay. It will only fit out of the bottom, it will not come out through the top.
The water pump on a 1994 Acura Integra is replaced by removing the engine accessories, pulling the radiator hoses, and taking out the retaining bolts. The pump can then be pulled from the engine block, the surface cleaned, and a new pump put in case.