Hello and welcome to V6Z24.
Most everyone is gone now and I'm certainly not an expert, but I'll try to help.
Yes, the engine is a direct drop in. The EGR is different though. However, I think your 89 EGR might bolt up to the 3.1 plenum. I've never actually checked that before. Other than that, everything may be okay. You should get the ECM from the donor car, along with the wiring for the later EGR, just in case. Another option would be to use the 2.8 plenum and EGR. Still the tune is most likely different for the 3.1. Having the ECM from the car the engine comes from, would be nice. But to use it without throwing a trouble code, you'd have to use the 1990 and up EGR. So, you would have to get the wiring in place. Hopefully the engine won't run lean using the 89 ECM and EGR. As long as it doesn't, everything should be just fine. It is certainly do-able without too much fuss.
You can try a search on the site to see if this has ever came up before. I'd imagine that people have dropped in a 3.1 to replace an 2.8. So maybe you can find some old threads to look over.