to FIX THE TIME LINE
the first movie goes the same but when Vanessa and Austin get captured and get future space outfits that Dr.Evil gives them, Scoot already kill Vanessa before Dr.Evil noticed and number two replaced her before Dr.Evil noticed and only told Dr.Evil when he got unfrozen in the third movie.
with the second movie and the Austin's Mojo issue, Austin never had his Mojo in the first movie. He got Vanessa though his charm without his Mojo, cause when you watch the movie Vanessa wasn't easily impressed by Austin at all, compared to Austin when he was in the sixties, And even though he didn't have his mojo he believe he did and over came it and save the world.
Austin lost his Mojo when he got frozen and learn to overcome it since the first movie. Vanessa was just replaced when Scott just wanted to kill Austin but mixed the rooms and found Vanessa's room when she was changing into her future space suit, and he kill her so when he couldn't find Austin's room. Number two just used an Fembot to replace Vanessa to fix Scott's mistake. so when Austin got married to Vanessa, she was suddenly all over Austin cause if you notice Vanessa didn't care for Austin much before and never really got charmed to by him. so she was killed by Scott since he just want to get his gun and kill Austin in the first movie.
At the end of the second movie, Austin of the ten minutes of the future that saves Felicity Shagwell goes back to the sixties with her and lives his swinger life out with her and many other women after his three-way with him self. the other Austin that joins the three way and after his other self leaves with Felicity Shagwell he just goes on to live his life in modern day life to see 2002 and to go back to see foxy, and that's my time line
and that's how I figure my head canon, if you like it, or question it, let me know and I'll figure it out or fix it.