Tighten all fuel system lines to the main, and swap the primer bulbs between the motor. An air leak or bad primer bulb could be your problem.
Could also be a VST or injector issue.
Here's a good writeup with pictures on how to change the VST (you can also clean it as opposed to replace it). It's not a terribly uncommon problem, and not as difficult as it looks in the pics.
A fuel pressure gauge is a good tool to have when diagnosing an EFI engine. It connects directly to the fuel rail, and you can monitor pressure when the issue is occuring. If pressure isn't dropping, you know it's not fuel related, at least up to the injectors. My guess is your pressure is dropping for some reason.
The injectors and screens can become clogged as well. They are super simple to pull, and fairly straightforward to clean, but I think your problem lies in the supply to the engine. If you aren't running a 10 micron fuel water separator, I'd change that over. Fuel injected engines are a lot more sensitive than carbureted when it comes to tiny particles in the fuel.