I would remove any references to "delaying" Judgement Day - I'd rather pretend there was no discrepancy with dates, and that history was set - the events of T1-3 simply being to lead up to what's already happened (and we're told the humans have just about beaten the machines in T1, the time travel being a last ploy by Skynet to change history). For this reason I would also have to remove the killing of John's "lieutenants" (the kids at the party) since that's changing history.
I don't know how you'd work around it, but in an ideal world I'd like to remove any mention of Sarah's death, as it smacked way too much of "the actress didn't want to come back".
Smartripper and DVD Decryptor will also let you run individual titles or chapters from a disc.
David