My 06 Frontier 4.0 V6, feels like it has a misfire at low RPM's between 40 and 50 MPH. This is the only time it happens. I've replaced plugs and wires. It hasn't gotten any better or worse. What else could this be

What "wires" did you replace? The'06 4.0 I have doesn't have any plug wires, it uses coil packs right on the plug.

This link on misfires should help:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-11.html#post2028083