Question on Computer Controlled EGR

[jagplates]

I have a 1998 Voyager with the 2.4L motor with 159,000 miles. It is California spec, with no EGR.
I just picked up a low mileage 1999 2.4L motor, equipeed with EGR and the ECM that goes with it.
I read that there was a computer firmware upgarde for the early 2.4L cars that improved driveablility. I installed the 1999 computer (with the 1998 engine) and test drove the car. The driveability does seem to be improved, but the car seems more sluggish than it was with the 1998 computer.
Of course, the 1999 computer logged a fault code for EGR failure (since the 1998 engine does not have EGR & the 1999 computer is expecting to see it.)

My question is this: When the ECM sees an EGR failure, does it retard the timing to compensate? Is this why the car seems more sluggish? Or does the driveabililty fix make the car slower?

I am trying to decide, when I put in the 1999 engine, should take off the EGR and use the 1998 computer? Or should I use the 1999 engine with EGR and the 1999 computer? The way the car is right now, it is noticeably slower on acceleration, and I would prefer not to sacrifice acceleration in favor of driveability.

[jagplates]

A bit of an update. The acceleration seems to be getting better (although still not as good as before.) Does anyone knw if these ECUs are the "learning type", that gather data about driving conditions for the first 50 miles or so, and then program themselves accordingly?