A start, if an overdone one
Madness flashes are dime a dozen here on Newgrounds. You're going to have to make a bigger impact with your flash to have it stand out. This is just another "guy A wants revenge on shady organization B" storyline, which is really week. The only difference is that this time he has a helmet.
The art is alright, but it may just be from a sprite sheet. The animation is jerky as well.
As for the .swf to .fla question - check your recycle bin. If it isn't there, you can just import the .swf into flash like you would any other file. That should do the trick.
Keep working. Once this is done you should try something non-Madness related. It'll do you good to work on original content with a more complex plot.