There, I've finally managed to pull this off! Took a bit in photoshop, but I now have images of both Edward and Naruto from Keys and Gates, of them as each other.
Writing-wise I've gotten to working with the story again, at least a little bit. I was bogged down by only having half of the plot down - Amestris's side. Now that I've placed the story into a semi-certain section of Naruto, I can develop Konoha's side, which I did before I made these images.
This story, as I've edited in the summaries of what I've put up, takes place after the FMA series, and thrown in (a bit randomly) during Naruto Part 2 (the manga). I edited chapter one, which mentioned Sasuke, to compensate this change in storyline. But now I have some real plot to work with.
Another thing is pairings. I'm fairly positive there will be at least hints of Roy/Edward and Kakashi/Naruto - the real them - but anything else may not really exist. And if it does, it won't be major, because of what I've done the plot will be the main focus over anything. I am still seeing a bit of Riza/Envy because I am so screwed up like that :3
So anyway. Images under the cut. There're two of Edward as Naruto, because I had fun with colors that I couldn't decide which I liked more. He's got the Kyuubi's chakra along with an alchemic flare behind him. Goes with some plot-points. Naruto as Edward was the more difficult one... He isn't supposed to have the forehead protector, but when I tried to clone-stamp it out, well, it came out horrible that I left it in ^^; So he's almost accurate.
I think I may still edit them later if I can find the right image to work with and give Ed a metal hand. They're both still flesh-and-body them... just switched clothing and got some skills tossed around, if that makes any sense.