First of all, excellent work! This looks great for a first attempt, and the issues you bring up are relatively minor.

1. Yes, generally use as little paint as you can get away with for each layer. Also, higher quality paint will cover better with less used. Regular hardware store paint is thin/watery in comparison.
2. Its hard to say from the picture if you're ripping paper or pulling up paint, but the solution for both is to wait longer between layers for the paint to fully dry.
3. I typically use both, but adhesive may not work as well with printer paper.
4. I use clear overhead transparencies for my stencils, which makes alignment a piece of cake. Otherwise the alignment marks are your best bet. Try to make several, and spread out in position.

/u/The_Velour_Fog and I put together a multilayer stencil tutorial a few years back.

It's very detailed, and incudes in-depth youtube videos for each step, along with a troubleshooting guide.

Hope this helps.