in photoshop/gimp, copy image, use black as transparency key, choose transparency channel, copy back to original image as transparency channel (e.g. set to only view transparency, then copy image, and in the original one add a transparency channel, select & view, paste back), then adjust gradiation of transparency channel till you've a good result, that's how I do it when transparency was lost
for mpr++ best would be to keep transparency, also for old hobs you can set semi transparency in palette.lst
that way they keep smooth. applying sharp edges doesn't look that nice.
But nice work with the torpedos as far I can see.