Guys, need some advice. I had the straight pipe exhaust changed to magnaflows and also removed the middle cat. Car is now running rough.

Should I reset the ecm so that it will adjust to the change?

Thanks in advance. Great forum!

First, welcome to a great forum!
That's where I'd start. Just disconnect the battery and leave it for a half hour, then reconnect and see how it runs. It's free and you can pass the time inside doing something else. Let us know how it goes.

If it continues, my thoughts would be to reinstall a good quality main cat, and get a mandrel-bent front Y that eliminates the two pre-cats. When I had my '88, that worked great as one of my early mods, and it also helped lower the amount of hi way "drone". I never had too much problem with running a cat, as long as it flows well. On the '89 I now have, I'm going to be running two cats off the headers. I guess it's my way to be a responsible car guy.

Honestly that in itself shouldn't make it run rough. Make sure there are no leaks in the area of the oxygen sensor and that it's hooked up/no burnt wires.

After that check to see if there are any codes.

I reset the ecm, drove it all day and it worked! Runs great now.

Thanks for the responses.