RE: Removing upper bunk....
Based on a couple of the responses to the initial question in this thread
apparently few have actually removed the upper bunk.  In addition to simply
pulling off the rear pad (it just snaps in) the rest of the upper bunk, the
part that folds, comes off with the removal of just four screws.  Pul those
screws and the rest of the bunk comes right out.  I suggest putting the
screws back into their holes so that they are there when the time comes to
put the bunk back in.
With the entire bunk out there is a space that is just 5 1/2" high for
storage.  Many options then for storing things. If trying to use plastic
bins you will have to do a little hunting at the local stores, most large
plastic storage bins are taller than the space you have. And also very
important, rig something to keep anything stored up there from coming out in
a panic stop or collision.  You really don't want a loaded box of 'stuff'
hitting you in the back of the head.  I posted a link to pictures of one
possible solution in an earlier post in this thread.