I forked the main bitcoin repo and made all the changes that are needed for the i0coin chain, i tested it generating a few transactions and even using the same blockchain that were downloaded with the old client and zero problems 
Did you backout the changes that result in blockchain forks? The BIP16 and BIP30 stuff? Or change the dates when these activate? If not, the majority of miners will need to be using your client, or problems may occur (anyone being able to redeem BIP16 transactions, working on an orphaned fork, etc).