I have made some progress, I finished the Gameboy processor emulator and got it to correctly pass all the test ROMs, and integrated it to extract the SML3 sprites properly from the ROM. Also I have finally added the static bonus sprites for power ups.
So the next stage is finishing the tile-set switcher (which works by simulating player movement across the level to decide which doorway was been used then applying the correct tile-set. This is practically completed already.
The editor is now nearly feature complete as a viewer, adding the editing after isn't actually a big deal, as all the hard work of figuring out how to do this has been done in the previous version before the rewrite.