I actually Just checked this thread out, and I like the Idea alot!
As for the Gyarados and Milotic OW's.
You could use the ones from PMD, and just recolor them accordingly.
Is this a hack of Fr, LG, R/S/E or what?
Cause there is a random sprite in R/S that is big enough to overwrite for the gyarados or milotic, then just sacrifice something else like kyogre or groudon for the other...