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Going from MMC1 to MMC3 is not a piece of cake. It involves a different way of loading graphics. You can probably use the same CHR swap as the original, i.e. swap 0x2000 bytes at PPU 0x0000 or 0x1000 in one shot. But the advantage of MMC3 is that you can individually swap smaller chunks of the PPU at any given time. I think the smallest is 0x400 bytes, which is a quarter of 0x0000 or 0x01000, or 64 tiles. That would make tile animation a lot easier and less "hacky".
As far as I know, MMC1 allows a maximum of 16 banks, so the expansion of banks is possible with MMC1. Just change the ROM's header, and then make sure the correct banks are swapped as needed. As for Zelda II specifically, you have to take bank 7 and move it to 15. I think the rest can be left where it is.
In Shadow of Night, the code for the Overworld bank swapping is at 0x2A40.