Some of it is trial and error (and a spot of luck), to be sure.
Some of it is this thread on the Gearbox forums. (EDIT: Ninja'd with link to the same thread. )
The unaccepted sidequests should all be available after completing Talon of God. Which is, conveniently, also the point at which unaccepted sidequests snap up to your level in P2.5, so ...
At worst, from what I saw in my own attempt to do the same, quests are temporarily disabled, but not permanently missed. You can't accept quests originating in Sanctuary from the time Angel betrays you until you get Sanctuary back in the Fast-Travel network. Claptrap's Sanctuary sidequests are unavailable whenever you have a story mission that requires meeting him outside of Sanctuary, and Mordecai and Brick's quests are disabled during Talon of God. You also can't do anything with Lilith's quests once you start Where Angels Fear to Tread Pt. 2 until you've completed Talon of God.
If you want a leveled The Bee with which to storm Hero's Pass, however, you absolutely must complete This Just In before starting Talon of God.