You got the right idea for tweaking the rotor but the wrong tool. Stick to just flexing it with your hands. The crescent wrench should only be used for repairing crash damage so you can get another ride or two from a disc. It's far too easy to flex the rotor way too far when using it for final rotor truing.

For the mechanical brakes to work well you MUST have the fixed inside pad all but touching the rotor. Otherwise you have to use too much of the lever pressure to flex the rotor until full contact is made.

If your rear rotor is not flat on the wheel I'd suggest you start by removing it from the hub. Check the seating shoulders and rotor spider for burrs or grit that may not be allowing the rotor to sit flat. Then check the rotor laid or held to a piece of glass and see if it lays flat or can rock around. If it rocks a bit when laid up to the glass on either side then your first job is to ease it flat again. Go easy, a little at a time goes a longer way than you think. Once flat then re-bolt it to the hub. Put the wheel back in the bike and see if the rotor is wobbly as it passes through the caliper. Gently but firmly flex the rotor with only your hands either out or in at the high and low spots until it runs nice and even within the caliper's slot. At this point adjust the inside pad towards the rotor until you get the lightest possible scuff at a point or two in the wheel's circle. A slight flexxing at the touching spots should reduce the scuffing. Then move the pad towards the rotor one more click. If it scuffs very lightly at two or three spots I'd say it's time to leave it. Don't worry about teh scuffing. If it's actually as light as it should be it won't slow you down at all. Besides, the pad will wear enough to make the scuffing go away after a few stops.

To adjust the point of engagement at the lever you need to adjust where on the cable the arm grabs. You can do this by loosening the pinch bolt and moving the arm on the caliper and then tightening it on the new spot of the cable. Smaller fine tuning adjustments are then made using the barrel adjuster at the lever.