I agree with Ron. Do you really trust that mechanic? I wouldn't, especially after the transmission diagnosis. The drop in RPM has nothing to do with it.
Why was the alternator changed? Was it because of your hesitation or did it have some other problem?
When was the last time you had a tune up? I've seen many of these problems related to old rotor, distributor, wires, and plugs. You can also test the coil. Start by checking these and afterwards the CIS system and injectors.