If there are no vac leaks, and everything else is good, then in this case it may be warranted to adjust the idle stop screw.
The Throttle body (TB) was designed for a 2.2
Now you are running 2.5 liters of displacement if I'm understanding.
it's a small 6mm locknut, with a tiny 3mm? allen on the screw to adjust the stop. Some have an 8mm locknut and a screw.......depends on what exact intake you have.
It's on TB with a little orange or yellow paint on it.
It is generally NOT a good idea to mess with that screw, but in the case of this frankenmotor it's probably your best bet for drivability. 1/4 turn or less should do it.
TPS idle switch contact may need reset/adjusted after changing idle stop screw.