Vanilla HiROM cannot load a 6MB game, 40-7f is a mirror of c0-ff. The only SNES PCBs to do that are well known: ToP and DKJM2 (SO uses a programmable mapper). Maybe one of those are close enough that you can rig things up, so long as the original game doesn't expect 40-7f to be a mirror (it probably doesn't). Feel free to look at the mappers for them in bsnes. I call them exhirom and exlorom, but they don't have an official name, as far as I know (and I don't care, so don't bother posting just to tell me, kthx).
You're going to need to write a recompressor for DQ3r. Due to the way DQ3r's text system is designed (load directly on demand), block decompressors like LZSS are out. I recommend
huffman + dictionary coding.