DNSDies did this swap for me and it turns out the SRAM is a problem. It seems Mega Man X has a copy protection that is triggered by checking for the SRAM. The issues I found were exactly as listed in this thread
http://jul.rustedlogic.net/thread.php?id=16940 after speaking with DNSDies I went ahead and clipped the SRAM off the board and it appears to be working properly. I was able to make it through to 3 different robot masters. I couldn't beat any of them but, this was farther then the game had allowed me to progress without out any of the protections being triggered. Everything seems to be fine but just an FYI for anyone else trying this swap you will have an issue if you have SRAM.
Shout out to DNSDies for helping me with the replacement and with the trouble shooting idea. Thanks a lot.
