Stuff like this is usually taken care of by the patcher but here goes:
The 00's and FF's that are attached at the end of the rom to make the rom image up the chip size can almost always be safely removed (you may occasionally have to give one or two back but this is incredibly rare).
If I have to do this manually I use GBATA after having renamed with a .gba extension: http://www.gbadat.altervista.org/tools.htm