Using a powered spawner to get a wither skeleton doesn't work, neither by capturing a wither skeleton nor by setting up a regular skeleton spawner in the nether. It seems like not even a diamond dolly to set up a vanilla skeleton spawner in the nether will work - you get some skeletons that are named wither skeletons, but they are just regular skeletons and drop regular skeleton items. I don't get exactly what is going on there, because it works in other packs (tested it in Direwolf20 1.7.10)
You'll just have to hunt for Wither Skeletons in Nether Fortresses like the rest of us do. You could use various tricks to speed the process up, of course, like using the sword The Ender from Ender IO with Looting enchants (getting specific enchants is pretty easy with EnderIO's Enchanter), or looking into Witchery's method of spawning the Wither. Finally, you just need to spawn a single Wither - you can transmute the Nether Star with ProjectE in the future.
As for the progressive automation miner, I just found it to be not worth it. It's better to just craft torches from blocks of coal and go mining like in vanilla. I actually set up a cobblegen - not by moving lava, but by working a cobblegen around an existing pool of lava. Then I realised that I can't actually automate mining that cobble without at least Erebus-Tier materials, and when I had those materials I just made a nether portal and made the philosopher's stone.
I'm somewhat mystified by EnderIO's travel anchor. Whenever I use it, I only rarely land directly on the travel anchor, but slightly beside it. This means that chaining multiple travel anchors together to jump multiple times is pretty annoying; and the range of the travel anchor ended up a bit too short for the way I built things, so I have to use multiple anchors. I know that Material Energy^4 has travel anchors where you land directly on top of the anchors, how do they do that?