So I have no actual building experience, but I have been to a cob workshop and rocket stove workshop as well as reading a good deal on the subject so I'll give you my knowledge on the first three questions...
1). Cob shrinks when it dries and this can create draft/structural issues if you put it inside the cob. You can refer to Becky Bee's Cob Builder's Handbook for this one (pole structure) I know for sure. I don't have the book handy but there is no issue with having poles to support the roof or house frame but you want to "cup" them with the cob, inside or outside the building, as opposed to inside the wall for structural reasons.
2) I don't believe it makes a difference what you build the second story out of, but cob would be easier. You don't have to worry about joining two different building mediums with deadmen or any other system if you build out of just cob because it is monolithic. No source for this one, just knowledge garnered from studying putting different materials together. The cob is more than sturdy enough to build two stories with. I've stayed in a couple two story buildings built with just cob.
3) It is suggested that you taper cob walls. The formula I got from the builder I worked with was taper 2 inches for every three feet of wall height. Walls should be about 9 inches at the top so measure the height of the wall and it's a simple math equation. I believe this info is in Becky Bee's book as well, and the Hand Sculpted House if I remember correctly.
Hope that helps a bit, and hopefully we can get some more experienced responses. I'm really interested in this as well! Good luck with the build!