I have a '94 2.5 YJ with the manifold on the left.
Today I swapped my TB with one of a 4.0L.
The flange opening in the manifold is about 56mm and the outlet of the 4.0L TB is 56mm.
By only swapping the TB's I increase the minimum air intake diameter from 48mm (outlet opening from the 2.5L TB) to 56mm.
I drove just a bit along the countryside today so cannot yet tell if it is a big improvement on the highway with a strong head wind.
I guess if you go to a full bore without changing the injectors, fuelpressure valve and possible O2 sensor, you might not gain extra power?
no point in changing the injectors unless you find them cheap - fuel pressure will be sufficient in your case. You should have some improvement but you need to make sure there are no other restrictions in the airflow (get a high flow filter, remove the tube in the airbox cover (called a velocity insert) and the inlet tube going into the bottom of the airbox.
not sure what you mean about full bore if that is a 4.0L t/b, or a 62/64mm throttle body - if that's what you meant then indeed you'll get better output by increasing fuel delivery, again the fuel pressure would be sufficient if you're only interested in wide open throttle performance, otherwise you're in closed loop and the O2 sensor feedback will cause the ECU/PCM to adjust fuel delivery and target 14.7AFR