I'll let Sandy answer most of your question, but I can say that the doctor's note was for bringing syringes and needles about. I don't think you will have any issue with the injection pen. Also meds in their original RX bottle are fine too. Sandy mentioned that if you need a refrigerator for the insulin then you can notify CCL and they will provide one for you.
I don't have any experience with the breathing machines so I'll let Sandy clarify her comment. But rest assured she was only trying to make sure you that you don't run into anything unexpected during embarkation that would ruin your cruise. (Like showing up with a box of injection needles and syringes and not having medical proof that you need them.)
Carnival Cruise Lines:
Fantasy 90, Celebration 95, Victory 05, Conquest 05, Spirit 6/06, Freedom 6/08, Holiday 7/08, Victory 6/09, Valor 9/09, Dream 6/10, Splendor 8/10,Conquest 8/11,Magic 11/11,Triumph 4/12,Spirit 7/12,Freedom 11/12, Triumph 2/13 - The fire cruise
NCL Dream October 2006, RCCL Mariner OTS June 2007, Celebrity Silhouette 2013