Not sure I would take a highly modified Viper to a dealer unless they have done Paxton installs and such before. It's easier to hook up a fuel pressure gauge (temporarily) than remove the pump assembly to change out the socks. I have not used an AEM ECU on a Viper, but I have on other platforms (3000GT VR4s) and have had two go bad. Those were earlier version ECUs and not the newer Infinity models.
Are the two additional fuel pumps turned on via a boost reference? Are you sure the other pumps are actually coming on?
The dealer is really good and has worked on plenty of modified vipers in the past, including a previous one I had, so I'm pretty comfortable with him doing some checking around.
All 3 pumps come in at the same time. When I had the fuel system done, I didn't think to have 1 or 2 come on at a boost reference.
The tuner says they are but I'll confirm because that would make the most sense to me, only 1 tuning on.
The car has been sitting for some time so thsts why we changed the fuel filter and had the injectors cleaned and will replace the socks next.