So the logo is in the MBC. I've erased my flash and the Gameboy still boots with the correct logo. Also found out that a read to address 0150 deactivates the MBC's internal ROM. Sanqui's 2048 would not boot on my MX cart due to no jump to 0150 at startup. Sanqui added a jump to 0150 and now the ROM plays fine.
CLK is not connected so the MBC is more than likely watching the bus for a certain address read. Cant seem to replicate it with my cart reader though. Might try step through the gameboy's boot rom via my cart reader to see what activates the initial ROM swap.
I have also cut down my MX cart to fit inside a standard gamecart, however now i cant get the original MX ROM to boot. I'll double check my address lines have not detached from the sawing of the board. Odd because MegaMan2 (256kybte) runs fine in its entirety. My replacements should arrive after the easter break so i'll continue investigating then.
AND!
I now have 10 spare Gamecart Reader/Writers available if anyone is interested. Get yourself one, and a Shark MX and you have your self a cheap Development Kit! Custom flash carts are in the works. Check out
http://www.bennvenn.com for details.