Since the computer that came with the car was speed density, you need to plan to do a mass air conversion. It should be one of the first things done before you make any significant changes to the engine.
Here's why...
Speed Density uses Manifold vacuum (MAP), Throttle position (TPS) and RPM, & Air Temperature (ACT) to guess how much air the engine is pulling in. Then it uses all of them plus the O2 and ECT sensors to calculate the air/fuel mixture. It is dependent on steady manifold vacuum and minimal changes in airflow from the stock engine configuration to maintain the proper air/fuel ratio. Change the airflow or vacuum too much and the computer can't compensate for the changes, and does not run well. Forget about putting a supercharger, turbocharger or monster stroker crank in a Speed Density engine, because the stock computer tune won’t handle it. Every time you seriously change the airflow through the engine, you need a new custom burned chip to make the engine run at peak performance.
Mass Air uses a Mass Air Flow meter (MAF) to actually measure how much air is being pulled into the engine. The computer uses this information and inputs from the O2, TPS, ACT, ECT, RPM and Barometric Pressure (Baro) sensors to calculate the proper air/fuel ratio. It is very tolerant of changes in airflow and vacuum and tolerates wild cams, high flowing heads, and changes in displacement with minimal difficulties. Larger injectors can be used with an aftermarket calibrated MAF or a custom dyno tune. This makes it possible to use the stock computer with engine displacements from 302-408 cu in, and make many modifications without a custom dyno tune chip. Put a new intake manifold on your 331 stroker and the computer figures out how much more fuel to deliver without having to have a new chip burned to accommodate the extra airflow.
Get the mass air conversion completed and running good with no codes and no problems. Otherwise you will never know if the new problems are a result of adding parts or a computer unable to cope with the engine modifications.