When you play a combo deck, you have to stick to your main combo in my opinion. There is only few deck that feature Emrakul, and there is no deck that feature progenitus (maybe some unusual elfs lists...), and for these emrakul decks you'll have to get your tormod's crypt, and activate it to the emrakul trigger. Of course it will be hard matchups, but all decks have bad matchups (+ for emrakul decks, you have back to basics, pithing needle... to tempo). Split to multiple combos will weaken each combo (less library manipulation, less counters...).
By the way, the list I proposed here have another awesome combo =>sensei+counterbalance hahaha. And the cool thing is that the sensei top is needed in this deck anyway and will be useful in a lot a situations (unlike dreadnought or stifle).
I hear people saying that it is better to not go with two different combos. I understand it isn't obviously a common practice. However assuming you were in a 2-3 game match and your opponent doesn't know what you are playing right away, if you went with plan A in the first game, they would probably sideboard for A when you can go with B in game two.
Also food for thought: if you have 8 cards in a 60 card deck that have a win combo such as: 4x Grindstone / 4x Painter's Serviant there is about a 16% chance you have a copy of both in your opening hand. Now obviously having cards like SDT and Brainstorm will help you dig, but if you also have another 8 cards in the deck that also have a 16% chance of opening with say 4x Thought Lash / 4x Laboratory Maniac tell me that isn't better odds of getting the win conditions you need to win faster? Surgical Extraction got you down on one combo, you can keep swinging!
Current list (stilll need to think about counterbalance):
2 Counterspell
4 Lotus Petal
4 Brainstorm
8 Island
1 Daze
4 Grindstone
4 Painter's Servant
3 Sensei's Divining Top
4 Force of Will
1 Academy Ruins
1 Maze of Ith
4 Ancient Tomb
4 Flooded Strand
1 Seat of the Synod
4 Fabricate
4 Laboratory Maniac
4 Thought Lash
2 Shelldock Isle
1 Mirror of Fate
//Sideboard
SB: 3 Hydroblast
SB: 1 Surgical Extraction
SB: 2 Grafdigger's Cage
SB: 1 Pithing Needle
SB: 2 Misdirection
SB: 2 Ensnaring Bridge
SB: 1 Trinisphere
SB: 2 Trinket Mage
SB: 1 Tormod's Crypt
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