Why does Merc 180e miss at low speed In first and reverse Alternator pops Runs ok once going?

The popping of the alternator might be a red herring. It sounded like it was coming from there, but, later, it seems to come from the empty space between

the exhaust manifold and the water reservoir. I could not locate it, but its an intermitent sharp pop, a bit like high voltage arcing (which it isnt).

The spluttering and missing can be extreme, in first and reverse, and at no other time. In neutral, it idles smoothly. If it was due to a manifild vacuum leak, it should happen in neutral also, shouldn't it?