My son's 1995 softail starts fine and runs fine while in neutral. Once I kick it into gear, however, it spits and chokes and coughs, with some backfiring like its not getting fuel.

Any ideas on what could be the problem?

 

First thing I would check is the fuel filter.
Next question does it get better after it warms up?
Another issue could be a stick float, has the bike sat a lot?