^ Sorry mate, it's a long discussion but a reversed engineered mmc1 does not mean it's the same as the real deal. It's the fpga that runs the mmc1 code and said code could behave differently in some cases. It's like early emus like Nesticle that was mentioned before - games run on it but it's still a very hacky job.
The only flashcart that can actually claim it's 99% close to original hardware is ikari_01's SD2SNES, it actually runs games like their real counterpart - something that the mainstream emus cannot achieve.
Take for example rockman X2: http://www.youtube.com/watch?v=0zpZbI6yS54
, sure it runs on emus and does not crash ever, but is it accurate?
I am not defending my soldering skillz or my famicom - not by a long shot - but testing on a fpga device is not a way of being 100% sure about something. It's very close to it but not 100% .
Your idea of testing on your real mmc1 cart is a great one btw, eventually you'll have to burn those eproms to bring it back to life with this awesome hack and have a nice original-looking cart