Nope. You shouldn't have much EEC trouble with a 1990. Vernon C. has done the trans swap in his car, which I think was a 1990, or 1991 and had no trouble running his original EEC. He is probably the expert on the early cars with regards to the trans swap. There may be a few slight calibration differences for a 5-speed, but you probably won't notice.
If you do run into trouble perhaps Brian of Apten can help with a chip, or pick up a used 5-speed EEC cheap.
When you really need to swap out the EEC is on the '94 and '95 cars where the EEC controls the automatic trans as well. It will run in a failure mode, reducing engine power, and ruining drivability, if the Automatic trans isn't connected to it.