Huh. That's a cool setup. I've mainly used self-sacrifice setups because I don't have a lot of experience building mob farms. Fluxed Electrum would be a lot easier to mass produce. Do you use another mob farm to get the mob essence for the autospawner? I had wanted to use an essence berry setup like I've seen Ako the builder use, but I still can't find any on our MF2 server so far. I suppose I should get more experience with making mob farms.
If you can do that (the above), you may want to look at trying out a Well of Suffering + trapped Witches combo when you hit Tier 4. I hear it's pretty popular for making an automated altar design. Is there a way to spawn witches in AgSkies?
Edit: For fighting the wither I would recommend a Talisman of Remedium from Thaumic Tinker to protect against the Withering effect. A Flask of Strength with a tier 2 or 3 power catalyst added to it would up your DPS a lot. Blood Armor should make it pretty easy to stay alive I imagine as long as you can protect against the withering effect (which will still hit you through the Armor I believe). I suppose you could also brew a Regen Flask to counter the Withering, but you'll definitely want some Lengthening Catalysts on that so it doesn't wear off in the middle of the fight (It's got 300 Hp if I remember right). But you can probably take it with less then all that depending on your MC combat skills. I personally wouldn't take the risk in a hardcore mode like AgSkies uses. I haven't fought him in my last two world playthroughs (my array of mods and then MF2) as I've never had enough wither skulls before (no mob farm skills again).
For the grinder, we have had a grinder set up on the vanilla drop trap that we have had going since pretty much the start of the map, that has just been farming essence. But if you can get cursed earth then its a lot easier (division sigil ritual creates the earth, which can be got as dungeon loot or from killing a wither). Each mob killed gives 100 essence, with 100 used for killing the mob. I also plan on building a slime farm which will be used for creating essence (fine tuning the design I have to work for huge slimes, but its not going so well atm, so I might just stick with large).
I'll do up a quick design tomorrow in creative mode and show you how to build one if you'd like, they are actually pretty easy.
Yeah, I just got my T4 altar, but haven't looked into the well of suffering yet, I might do, but as far as it goes the design I have works wonders for me because I know I can keep up with the blood I need for the rituals/keep my network full for a long time with the 300 odd endermen that spawn!
(I also can also disable it if I don't want to burn through all the essence, but I generally don't bother as I don't need to refill that often.) Not sure about a way to spawn witches though, although if you can that'd be pretty awesome to know.
Sadly, TT isn't in AgSkies, but I've played enough vanilla (and killed enough withers in modded) to know how to take em down easily enough. A flux infused sword with Smite V on it takes em down in no time at all! (Smite V sword is a must for taking down the wither imo, it litterly rips him to sh*t!)
Haven't looked into the alchemy side of things yet with Blood Magic (really only did the quests, and upgraded my altar and made the sword, but dayum did I have fun even just doing that, and I can't wait to get into more of it!)
As for farming wither skelly skulls, even if you don't have a mob farm, you can capture one in a safari net and set them to spawn exact copy, and you can use an XP extractor to take a level of XP from yourself and give you a bucket of mob essence, which is enough to spawn 2 wither skellys, that with a cleaver with max beheading should give you a fair number of skulls to work with.