Method 1, step 16 says to pre-drill a hole at each end of the line, screw in two screw eye hooks, and adjust them so that the eyes are parallel. What does this mean?

It depends on what the wall is made of. If it is wood, it will be very difficult.

It means to work the final row with the right side facing you (rather than the wrong side).

Nope, nothing to add. If you want it right and permanently so, then you'll have to remove it and re-level and re-tamp your base material. It won't ever be right...

A hole/paper puncher can be used for putting holes in the sticks. You can also use a nail and hammer.

The tip of a screwdriver should work.

Straighten the paperclip, slide one end into the hole, and feel for a button on the inside of the lock of the door knob. When you find it, push.

Depending on where the screw is located, you may be able to do this. You can just drill straight into the same hole the screw is in. If you're lucky,...

If you don't, the drill rotation will send the key flying out of the drill when you turn it on.

Always put an extra one for good measure.

For the initial drilling, you want to measure the diameter of the screw's threaded part. For the countersink, you measure the diameter of the screwhead on top.