For NOOKcolor and books that don't stop downloading, you might try powering off the NC and re-trying.
1) From what I can tell, books that are downloaded into the Nook are entirely separate from those downloaded to the PC - i.e., you need to download the book onto your PC to read it on the Nook for PC app.
2.) is your wireless connected for sure?
3.) haven't run into
4.) don't know what you mean