[tomj76]

There's not much information in your post to go by. It really could be many different things. Anything from spark issues, fuel delivery, emissions control, timing, air flow...

Check your air filter, since it's easy.

It's hard to know if the problem is due to changing the fuel filter, or that's just a coincience. You could focus on that for a while. The filter is not that expensive, so you could try a different one to see if that can cure the problem. I don't know if you could temporarily eliminate the filter with a direct connection from the tank to the fuel line, but that would be another way to eliminate the new filter as the cause. However, be careful with that approach as any dirt in the tank that would normally be caught by the filter will clog your injectors and create even bigger problems.

I've had misfire issues due to clogging of the EGR ports, which you can only check by removing the upper intake.

The spark plug wires or a bad coil can cause misfire.

Sometimes the torque converter clutch in the transmission can chatter, which can feel like a misfire or shudder. I know it doesn't help much to have such a wide varying list, so maybe you can learn some more to narrow down the options.