The normal Greddy theory of operation is that the stock engine management (consisting of stock ECU, stock 19550-1970 212cc fuel injectors, stock AFM, stock FPR) handles fueling when not in boost. In boost, the fuel injector pulsewidth will be maxed, and the only way to get more fuel into the engine is to increase fuel pressure. That is the job of the Vortech FPR. The Vortech FPR should have no effect before spool up.
Significantly, RX-7 fuel injectors MUST NOT be used with this setup unless you have a programmable ECU to control them. Otherwise, you will just flood the engine when running open loop, such as when you stomp on it at low RPM. The RX-7 19550-5740 440cc fuel injector has a blue top. If you've got those in your car, it would be bad. 440cc >> 212cc.
Here's a website that might help you out: http://miataturbo.wikidot.com/fuel-injectors
So, your task is to make sure that everything is stock and functional (preferably by diagnosis rather than parts replacement) to handle the sub-4K region:
1. Fuel injectors good and correct part number?
2. ECU good (only way to determine is to swap -- do you have a friend with a Miata)?
3. AFM and wiring good (check with multimeter)?
4. FPR good (check with fuel pressure gauge)?
5. NBO2 and wiring good (check by comparison to WBO2 in steady state closed-loop conditions out of boost)?
6. MSPNP uninstalled correctly. For example, was the IAT sensor removed and stock wiring 100% restored to the AFM? Was the 10A ST SIGN fuse put back in? etc.
Keep in mind that the 1.6 is naturally low on torque below 4K. This is exacerbated by the following:
1. Your engine may be tired.
2. With the Greddy install, you are supposed to retard your timing 4 degrees to 6BTDC. This kills the low end.
3. If your timing belt is off a tooth or two, the "peakiness" of the engine can become really exaggerated.
I was happily running an MSPNP with large injectors and no AFM long before I ever installed my turbo. There is no way I would run bandaids like the Vortech FPR, a high pressure fuel pump or an O2 clamp. Too imprecise. The only parts of the Greddy kit I used were the turbo, exhaust manifold and downpipe. The only part of the Greddy kit I used without modification was the turbo.
If you do ever re-install an MSPNP, you must permanently remove the ST SIGN fuse and you must unplug the ignitor anytime you flash new software. Otherwise, you will kill the MSPNP and/or the ignitor.