Help Diagnosing Transmission Issues

Hey Friends,
New to the TacomaWorld forums and not every mechanically inclined so please let me know if I'm in the wrong part of the forum for help diagnosing issues.

My 2006 PreRunner 2WD V6 4L is at 300k miles and I just started noticing some mild "bumps" when I'm driving. I recently towed a boat from Fargo, ND to Durham, NC and accidentally drove in D (overdrive) instead of 4th gear for about an hour when i first noticed the "bumps". Now a week later, I'm feeling these bumps when driving without a tow load. The bumps usually come in sets of 1 to 4 about half a second apart.

I was fairly certain that this was a transmission issue but noticed these bumps happening when I was stopped at a red light. Can you please help me figure out whether this in an engine, transmission, or differential issue?

 

If you're feeling it when you're stopped I don't think it's transmission related. When were your spark plugs last changed? Typically when they're worn right down and gapped a mile wide they'll cause subtle misfires. Any codes stored or pending?

 

I don't see the check engine light on right now although it did come on momentarily when I was towing the boat. I assume that this means there might be a stored code. I'll see if I can get my hands on a diagnostics tool to see what it says.

The spark plugs were last changed over two years (~30k miles) ago. I can take a look at them next time near the vehicle.