Did you do any work on your car immediately before you started noticing this problem?

It is strange that the stumble in the engine only happens when you are in 2nd and 3rd gear. Can you try to accelerate slowly when in first gear to see if you feel the bogging/misfire. Then the same in 2nd gear. Try to figure out the rpm range when you feel the engine have a problem.

If the rpm range where you are having the issue is 1800-2200 area, then clean the EGR ports on the intake manifold. This is pretty simple to do on the EX engine.

 

PAHonda. No work was done just before this started happening. I filled the gas tank as normal on my way to work and it started within the first 75 miles or so of that fill up. Beginning to wonder if I got some bad gas. Going to change out the fuel filter and run a can of dry gas and injector cleaner through it and see what happens.