If you have both the Holley throttle body and the Holley intake it's already an improvement over the stock design. The throttle body has a much larger bore and the single injector's output should be increased with it's stock setting. With it having the much larger runners going into the engine it'll improve fuel and air delivery. Personally I would just install the components, run them as-is to ensure they are operating correctly, then from there seek out modifications to fuel pressure if it is desired.
All the Fiero transmissions are geared for when US interstate speed limits were 55 MPH. That is why your three speed auto was revving so high, because obviously you're not going to be driving 55 MPH on the highway (usually now it's 65 - 75 MPH). I always thought the five speeds rev'ed lowest at high gear
as you have more gearing? I would think the four speed used in the '84 models would still rev high, but personally I have never driven a four cylinder Fiero with the four speed - only the five speed Isuzus that four cylinder cars got starting in 1985.