Are there any programs that will allow me to remove the stubs that dop IOS mod marks as useless?

More specifically, IOS's 222 through 254 (i think) which are the ones are piracy protection.

I believe these are the cause of my problems with installing cIOSCORP.

I am on a 4.0u system menu downgraded from 4.2u to 3.2u, then re-uploaded to 4.2 then downgraded to 4.0

Any help is appreciated.