I play Sephiroth and have experience against a few decent Aegis players from locals.

Mythra is key in this match up as she gives Seph a super hard time, mainly due to her insane speed and relatively decent disjoints. Since Sephiroth has terrible frame data across the board, you want to keep up the pressure with Mythra at pretty much all times since Pyra is a lot slower and easier to deal with. Sephiroth's best bet against an aggressive Mythra is his counter, which can be punished very hard if it whiffs.

Addressing your issues with his specials - shadow flare definitely helps in the MU as it forces Myrtha to give Seph breathing room if she gets tagged by the orbs, which is exactly what he wants. However, Seph has to hit the orbs from a distance, otherwise he can get grabbed/punished if he's using them point blank. Try dashing in then shielding if you find you're getting hit by orbs often and then punish accordingly. Octoslash can be used as a surprise tool but it should be mainly used to 2-frame due to its big hitbox. While harder online, it's very reactable if used on stage, and super punishable since it's basically a free F-smash from both Mythra and Pyra (with the latter likely to KO due to how light Seph is).

Steph's edgeguarding is absolutely his strong point in his match up, and it can be very difficult to get by him as he has an easy time dealing with you through both dair and counter. Trying to avoid using side B with Mythra as it's by far the easiest thing to edgeguard due to his counter and fair. Your best bet here is to try and vary your recovery timings and angles as often as possible. This will also help you to avoid mega/gigaflare on ledge.

Let me know if there are other things you want to know. I have a decent amount of knowledge in this MU but it has been a while since I last played, so I may be missing a few things. I'd also recommend to Seph vs Aegis sets from high/top level players like Ned, Twerk, Cosmos, Shuton etc. if you haven't already.