Cleanup turns to mess up. Need some help troubleshooting.

Have you pulled a spark plug yet ? Gas soaked plugs will not fire, another thing I have not seen you post, Have you pulled a plug wire off a spark plug and seen if it is firing ?

I haven't pulled it yet because it fired up and ran just fine, as well as I didn't touch anything on that side of the motor throughout this whole process with the exception of pulling the valve cover.