While there is no standard legal format for a will, I've yet to see one which doesn't commence with something along the lines of "I hereby revoke all former Wills and testamentary dispositions made by me." If the 2005 document included that phrase (or something similar to it), and was properly signed and witnessed, the 2001 automatically ceased to have any validity whatsoever. (That would hold true even if the rest of the 2005 document was so poorly drafted that it was completely nonsensical).
Any codicil dated 2009 would not be valid if it specifically stated that it was a codicil to the 2001 will (since there was no valid will, from that date, to append a codicil to). However it would probably be valid if it only stated that it was a codicil 'to my last will and testament'. (However, anyone drawing up a codicil which doesn't cite the date of the will shouldn't be doing the job!).
It appears that your stepmother has committed a serious criminal offence by making a probate application based upon a will which she knew wasn't valid. The advice, above, to involve the police may well be sound. However you might not get very far if you walk into a busy police station on a day when everyone is engaged in more pressing duties. Try inviting your local community constable around for a cuppa. He/she will probably know next to nothing about fraud but he/she will know who to discuss the matter with at the police station.
Chris
PS: Anyone who retains an old will (perhaps for sentimental purposes) should always write 'Revoked by new will, dated xx/yy/zz' across it. (I've done exactly that with my old will).