Sorry you are having so much trouble. I have disk brake bikes and have no trouble removing and remounting them. Something isnt quite right.

One step left out of the guide you posted a link to, is AFTER making the adjustments they demonstrate, hold the brake ON and loosen the mount bolts, then re-tighten them. This will make the caliper more parallel to the disk than just eyeballing it. That might solve your problem.

-SP