ok the stock efi system is damn near bullet proof because it's so simple. Have you done any modifications? like shaving the intake or removing anything that could effect normal operation like the EGR valve?
If not then I would start by checking all vacuum lines, then the electrical connections, then testing the resistance of sensors. You should literally be able to solve almost any problem related to the EFI with what I just said.
It could also be something like your coil is dying, or you have blockage in your exhaust (old exhausts tend to rust and flake off impeding your exhaust flow), or even timing if its really bad.