89 Chevy 2.8L #3 & #6 misfire.

The ignition modulator may have to be replaced, you can pick one up at Auto Zone and it's still pretty expensive so you may want to try the Salvage yards. The ignition modulator's are common interchangeable part for the GM line so you can get one from a newer car then your 89 cavalier. Good luck and hope this helps. I believe Auto Zone can also test the ignition modulator too, the modulator is what the coils sit on. 

Swap the coils see if problem moves to another cylinder. You can go to a junk yard and get another or autozone. There are also MSD options for that car. If you get MSD I reccomend plugs and wires.

Its unlikely but,...... Has happen before that you got a bad coil from where ever it is that you bought it from,

I have heard a Crank shaft Sensor can cause misfires but, it's Hard to tell if that's the case:/

You replaced the Coil, Wires and plugs?