But that is easy, just use an xdelta patch instead of IPS, which can overcome your problem directly. Plus if you do decide for IPS there should be no problems, since the editor did not fill those 3 additional MB completely. In fact most of them are probably 00 bytes. Making an IPS based on the expanded original rom is not recomended, since there is no reason for it. This might be necessary if your rom would be 6 or more MB.