Two things of note here: my luthier shimmed the neck using sandpaper and he put D’addario strings on. When I played the guitar in the shop before I bought it, there was either no sustain issue or it is possible that I just missed it. It sounds like my priority should be: put a full wood shim in the neck cavity at the same time as I put different strings (elixirs) on as well as a higher end bridge. What do you think?
Sandpaper? As in sticking in a piece of sandpaper as a shim? The DEFINITELY replace that with a wooden shim. Sandpaper means ye not only have a different material (silica) but ye also have the microscopic air gaps between the sand grains which will act as a barrier to the transfer of energies between the neck and body.