I have the CDs for "Lighting Their Darkest Hour" and the 20th Anniversary reissue of the original Soundtrack album. I used those to create the isolated score.

"Lighting Their Darkest Hour" has the complete score, including tracks that weren't included on the previous score album but it omits the unused audition track. My only gripe is that all the releases use the version of the "Autobot/Decepticon Battle" track that appeared on the original soundtrack and not the original source score. It fades out early at the end so I had to do a lot of work to reconstruct the correct fadeout for the isolated score.

Most of the tracks in-film were edited differently from what was on the soundtrack albums, so the isolated score will be quite different from what is on the CD releases.