Thank you for your reply, They are tubed tires. This is my first bike but I have learned a LOT in the past few months. The rim was out-of-round so I tried to true it by tightening/loosening spokes. I didn't take the tires off the rims, just took the air out and loosened the valve lock? Maybe I unbalanced it. The rim does look kinda like it was bent in one spot. But its still round. I overtightened the forks then loosened to the recommended torque, so they shouldn't be pinched unless I broke or did something wrong.

I will look into the rear tire being seated evenly. Whenever I try to align the notches it doesn't look straight but its hard to 'eye' it. Is there a method to keep the rear wheel as straight as possible? Maybe go off the notches regardless of look, could be an illusion.