What kind of fuel pump are you running, its definitely starving for gas. You'll need at least around 40 psi, and a fuel pressure regulator. My Toyota twin cam powered Morris Minor was doing the exact same thing. Turned out to be rust in the tank clogging the fuel pickup. Have you tried hooking up an oil pressure gauge in line on the pressure side of the system to see if your losing pressure? Or unplugging the fuel return from the tank and measuring flow. These tests should lead you in the right direction.
Also, it will never run right without any sort of management system. Fuel injection relies on multiple sensors (in your case you should have TPS, O2, And either a MAF or AFM (the maf is built into the mega-squirt)). 14.7 air-fuel ratio is pretty impossible to attain without management. If Drastically off from this golden number, the motor will either bog or stall. How much flow is your injector capable of?
