I have a professionally built ej22 frankenmotor (90 heads and ECU) in my vanagon

one of the nagging issues is a persistently low idle (~500rpm) causing an annoying rough idle and vibration, at ~700 rpm the engine is perfectly smooth.

I recently hooked up my AC which would occasionally make the problem worse by stalling the car. To my surprise i discovered that the builder already applied a 12v signal to the AC wire at the ECU in an attempt to raise the idle.. I have played around with the IACV as well as the air bypass screw and it runs perfect, but the ecu eventually re-learns and drops the idle back down. What other things should I try in order to solve this?

A lot of variables in this one, but unplugged/cracked vacuum lines can cause issues. 

5 hours ago, wtdash said:

A lot of variables in this one, but unplugged/cracked vacuum lines can cause issues. 

add to that age/heat hardened ones.. they don't seal anymore.

it is worth the few bucks to buy and replace vacuum lines if it has not been done. just buy several feet of the appropriate sizes and cut to length using the old ones as a guide

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.

the Idle control valve/motors do fail from time to time.

When i have annoying issues like this i usually swap the whole intake. This eliminates over 1/2 of the potential problems all at once.