I have 1991 forerunner that I need an engine for. I have a 3.0 from a 94 lined up to buy. Is there anything I need to worry about? What has me most concerned is that rock auto list the two years as having different ecus. Will the 94 motor run on the 91 ecu?

 

As far as I know the ECU should work fine with either year. The main difference you might run across is a hydraulic belt tensioner on a 94 instead of spring loaded on a 91. There's a possibility your head is designed for a distributor with a different length shaft as well, I don't remember at all what years it affects. Some heads have a small divot that the end of the distributor sits in and the dist for these is about 1/4" longer and so won't seat in a different head without the divot. Again though, I'm not sure what years had what with this issue

 

I have swapped a lot of engines over the years, that much of a difference in years will mean that you need to take all of the electronics off of your original engine and swap them to the replacement regardless of any other surprises you might find.
Not sure about the 3.0 specifically, but in general you find that the block and heads are the same and everything else changes over the years. I have even done swaps where both cars were the same year (Honda), same engine, same trans, but one was a DX and one was an LX and there were different wire connectors on alternators and some of the sensors, so my plan of dropping the entire drivetrain, subframe and suspension assembly from two vehicles and putting one back together left me still having to go back and remove parts that I didn't think I needed.