I've told you twice now that GBA files cannot be run on the MMD. At all. Please stopt trying. The header thing only applies to .ds.gba files, which are actually DS binaries to begin with.
The GBAMP you ordered can launch small multiboot GBA files since it can load them directly into the GBA's RAM. There is a partial list of such files at
http://wiki.pocketheaven.com/List_of...ultiboot_games
As long as you got the CF version, you can run special versions of PocketNES and Goomba Color that will let you run NES and GB/GBC files larger than 256 kb, normally impossible due to the RAM constraints. This is because they use a paging system that calls up specific parts of ROM into RAM as needed. This means however that some larger games will be constantly swapping the working set, causing noticeable slowdowns (called "thrashing").
EDIT: I realize now that my first paragraph here was really rude. Sorry about that. Don't take it personally, I'm just in a bad mood right now.