Thanks for the post on your results. It seems confusing, to me anyways, That you say "with the new pads, the problem got even worse, and I noticed the wheel is hot again." Seems the problem has not been solved. I will assume that you changed both sides[driver &passenger] pads. What was the condition of the other set? You also say "no sense in ruining another rotor". Was the rotor groved or otherwise ruined? When you apply the brakes does it seem like the car is riding on oval shaped tires?
I also had the thought that you are saying you are planning on taking the caliper apart...is this what you mean by "thinking of taking out the caliper".
Did you have time to check the other components as suggested in the above posts? Wheels balanced? Check the struts? Have you had the motor mounts checked out? I might suggest doing some of those first. Good luck!