Hopefully none of you will have to do this... but if you have to I happened to try this out of desperation and it works. If you ever have to transport your bike while the engine is apart...i.e. the upper end is removed and the lower end is open to the elements or is seriously damaged from crash etc...don't try to rig up a bunch of plastic bags w/ tape and rubber bands...yes I tried this first. It was lame and would have ripped apart quick. Instead out of necessecity I took an old fleece jacket and literally zipped it around the engine. Place the jacket with the the front zipper openend and facing the ground. Zip up below the skid plate and thread the arms through space just in front of, and behind, the carb. It completely seals up the engine and keeps out unwanted dust and debris. Obviously this is for short jaunts and you should still stuff a good rag in any open spaces but this really helps protect the engine from the elements. Hope it helps someone at somepoint.
Cheers