Factor-X #3 has a few flashbacks that are currently split up in various character chronologies.
FX 3 (15:1-15:2)-FB
-Cyclops captures Jean Grey and Sinister begins to experiment on her (Jean is in her pre-Sinister suit)
FX 3 (15:3-15:5)-FB
-Weapon X breaks Jean out of Sinister’s complex; Cyclops tries to stop them but Weapon X cuts out one of Cyclops’ eyes
XF 3 (9:3)-FB
-On their way out, Weapon X and Jean run into Sinister (this is before XCHRON 2, where Weapon X and Jean Grey are with the X-Men, and Jean is in her post-Sinister suit)
FX 3 (7:2-7:4)-FB
-Weapon X fails to stop Jean Grey from returning to the X-Men (this is after XCHRON 2, where Weapon X and Jean leave the X-Men)
On the Age of Apocalypse page:
CYCLOPS
AOA:SB-FB
XM -1-FB
AOA:SB
*FX 3 (15:1-15:2)-FB
AOA:SB
*FX 3 (15:3-15:5)-FB
AOA:BL
XM 1-FB
{X:ALPHA}
…
GREY, JEAN
XCHRON 1
XCHRON 2/5
*FX 3 (15)-FB
*FX 3 (9:3)-FB
XCHRON 2
*FX 3 (7:2-7:4)-FB
{X:ALPHA}
…
SINISTER
XM -1-FB
AOA:SB
*FX 3 (15:1-15:2)-FB
AOA:SB
XM -1
XM 4-FB
XM 1-FB
*FX 3 (9:3)-FB
{X:ALPHA}
…
WEAPON X/LOGAN
XCHRON 1
XCHRON 2/5
ASTONX 3-FB
*FX 3 (15:3-15:5)-FB
*FX 3 (9:3)-FB
XCHRON 2
*FX 3 (7:2-7:4)-FB
{X:ALPHA}
…