The professional approach is always to scan the engine and compare to specs. It is also useful in cases such as this to carefully compare the data to that from the other engine. To do this you will need a scanner and the Diagnostic manual for the ECM (computer) on your engine. The ECM will be an MEFI (2 or 3 or 4, etc.) depending upon the year of manufacture. The Diagnostic manual is also very useful in understanding the operation of the engine and trouble shooting, even if you don't have access to a scanner.
The scanner is useful for most trouble shooting and occasionally is the only way to find and correct problems (such as with the infamous "cam retard" adjustment).
You did not mention scan data so I assumed you do not have a scanner. My suggestions were based upon experiences I had with a similar MPI engine. And in earlier engines (mine are 2003), injector performance and individual cylinder spark performance is not monitored by the ECM (engine computer).
You can check out Mark's suggestions of the manifold air pressure sensor or the engine coolant temperature sensor with a scanner, or you can simply swap them between engines and see if the problem moves. They are a quick and easy swap.
What year are your engines? Have you had occasion, for any reason, to loosen the distributor clamp (this would change the cam retard)?