Yeah, you're absolutely right. I'll put some more work into it; I'll mess with different combinations of layers, adjust their opacities, and use erasing tools to get it to the point where it looks about right. Thanks for pointing me in the right direction.
The front art? Yeah, the retail cover is off to the right a bit more. But I had to rebuild the whole thing because there were lots of elements in the original scan that I couldn't clean up properly, and the front image was part of that. So I tracked down the artwork Capcom used for the cover, but there isn't a copy anywhere I could find that shows more of MegaMan's buster on the left side. The image you see is just barely under the GBA border overhang on the left and can't be moved over any further. But I also never liked the fact that everyone on the cover was off-center to begin with (Team Colonel has the same problem, and it's really odd to see MegaMan basically crowded mostly off of the cover of his own game), so even though it's not retail-perfect, I prefer the aesthetics of having the art properly centered. But if I can find another version of the cover art that has the left and right borders expanded, I'll make another version of the cover with the retail art orientation.
Thanks for your help.