1. I believe bikes come from the factory with thread locking agent on the sprocket hardware so take that as you will. I'd use the loc-tite blue instead of the red. Blue won't be as difficult when removing the hardware next time.
2. From the way you describe it, Kinda sounds like your rotor is bent or warped. New rotor for your bike is about $115 (Braking brand).
3. Setting the chain adjusters on both sides of the swingarm to the same mark works ok but there's also a tool you can use that slips into the axle bolt. Either way, when doing mine, I put a small screwdriver betwwen 2 teeth on the sprocket and rotate the wheel back. This tightens the chain thereby pulling the wheel forward against the adjusters and holding it there while I tighten the axle bolt. Then remove the screwdriver.