Great job with the port! But I may have found a bug or it might be something I did wrong, I'm currently unsure...
I built a reproduction cart for myself using a board from MouseByteLabs. I used a 2mb 27c160 for the ROM chip and programmed the last 512kb on the chip with a copy of the final 512kb of the ROM.
The bug I've encountered is that I can boot the game and play just fine, but if I turn the game off and try to turn it back on it will not boot. To fix this I need to insert an original cart, boot it up, and then try booting Metal Gear again and it will work.
Model 1 Genesis with a model 2 Sega CD attached if that's any help, and again great job on the port.