The marks you made are assuming that the alignment was correct in the first place. If had been done recently and you feel the alignment is ok, well then that is up to you. Be aware that an alignment can "feel" fine but still wear the tires.
You may have had some loose hub bearings allowing the rotor to wobble slightly against the pads causing the noise and that is why when you replaced the hubs the noise diminished greatly but you still see the wear pattern on the pads and rotors. If you can afford it get yourself new rotors of good quality and new quality pads. If you machine rotors they get thinner and if have hot spots they will come back quickly to the surface of the old rotor. Friction is what slows you down, friction builds lots of heat, heat transfers in to the rotors and pads and if the rotor is machined thinner it will not dissipate the heat easily and they will warp and then you have the pulsation effect when braking, like from highway speed on an off ramp.
You have spent a lot of time in there and want to be done with it. Again, make sure you clean all rust away and lube all contact points with high temp lube.