I have had my Warrio's Woods prototype for about a year and I am trying to get my butt in gear and start documenting any differences. I dumped it when I first got it and I compared it at the binary to the released version. It is different but after hours of playing I haven't seen any difference. I and the person helping me (http://www.nintendoplayer.com/)  are thinking about approaching the problem from a different angle. If we could identify what the code with differences does then maybe it would be easier to document the prototype doing it differently. Sadly my 6502 knowledge is crap. I need the community's help figuring out what these differences might be doing. There are two main areas with different code 

Can you post the lines 1 before and 1 after to? And make it much bigger. Or even better, grab 6502d and use it on both files and look for those pieces of data in the ROM at the real programming changes rather than transcribing the byte code by hand.

I'll try 6502d and report back.

Okay cool, one of the best ways to find out what RAM if for is to play the game and see when it updates, how oftenn, and try to narrow it down what it may be used for. Hope that helps. If you need more and I can try to look into it, but I won't dive down into starting to disassemble all the code, I'm kinda busy with other stuff right now and haven't really done such a thing yet all the way through.

OK Try 2 from 6502d I gave a bit more leway, and blued the different lines. Thanks for your advice 3gen.