[Ibby]

+1 for what Death March mentioned. Any electric motor will spark to some degree. The particular motor that TOP uses will spark quite a bit. Cleaning the brushes and commutator as mentioned above will reduce it quite a bit if done properly. It's a very simple job to do. The other nice thing about TOP 249's is that a lot of RC car motors can be bought that fit in the mechbox easily. As for cleaning out the metal filings from the motor, I'd recommend using automotive brake cleaner. Just go to town on the motor with some and it'll be clean as a whistle. It will remove any grease and loose debris, so you may need to regrease the mechbox when you're done.
The smell is quite normal as stated above. New motors will smell a bit when they're first broken in, and can smell later on if they encounter a higher than normal load or grease or oil get in them. Good luck with your gun!