Disappear, from start to finish, almost makes me burst into tears whenever I hear it.
It's the one song I will *never* listen to in a public place.
Honor Thy Father. Still one of my favourite songs from them, from my second favourite album!
1) If you search "John Myung rig rundown on YouTube there is a video that details his whole set up.
2) The Ibanez GSR206 is a good value six string that rocks in at about 300 euros if I counted right.
3) Tapping on a bass requires some precision in the way you hit the string to even make a decent sound, and getting any speed requires huge amounts of practice. If you're a beginner I would say leave it until you've been playing a while.
4) Writing music is a very different skill to playing, so keep trying different things until you see what works well. For writing a bass part, you need to remember you're the rhythm section; JM may play all sorts of fancy bits but you need to always lock in with the drums, and in act heavier music you need to support the guitar by playing notes within their chord, probably the root.
Hope at least some of that helped :)