About the Twilight Forest and how to balance it and keep it useful.
I have no idea how much you are able to alter, Drastic, but I'm just going to pop some ideas hopefully to inspire you.
In my opinion flight should be pretty end game content used for killing the dragon, exploring the End and for plain convenience in moving around.
So to obtain flight, from any mod, one would need an item that is only dropped by the ur-ghast. It is used in the recipe to create said flight item or spell and has a 100 percent drop chance.
Reasoning: the Ur-ghast difficulty decreases the most with flight imo. It will prevent players from flying up the tower and killing it with no effort because the ghast can't damage players when they're flying. And because of the progression in the Forest it makes sure people can't use flight at the naga, lich, minoshroom, hydra and knight phantom. Most of them don't suffer that hard from flight, but the lich and the hydra do.
I haven't played much with the yeti and the snow queen but I think the snow queen has the same problem as the ur ghast. Maybe make the snow queen drop said item. You can do it with every notable piece of equipment one can get.
Like a fiery blood to create a soul forge for bound armour, this even makes a bit of sense since its blood magic and one would need extreme powerful blood for such a powerful set of armour.
The real challenge is to keep players in the overworld for a bit and allow them to build a base in the safe Twilight once they at least have beaten most of the bosses. You don't want people to find a twilight portal early game and cheese through the early stages of the pack.
Also, please don't ever remove the Twilight Forest. It has got the best trees of all available mods and generally a magic-esque feeling to it, even more than a magical forest from thaumcraft...