I have been using a modified version of this deck and upgrading it. I have ~33 upgraded cards. This is what I would do based on what I have noticed does and does not offer an impact after upgrading the card.
-Drop 2 dials for 1 more quintessence and 1 more bone wall. Immortal oty is KEY for this deck so you need 1 more quint in order to assure you get it early. Never ever ever use your first quint on anything but the Oty. I also dropped protect artifact and added 1 more dimensional shield. This shield is uber (3 free turns). Protect artifact is only useful against 2-3 FG that I found I could not beat anyway because they start too fast and this deck, unupgraded, is too slow. I'll add a protect artifact back in once I have fully upgraded.
-Upgrade the key 7.
-Upgrade 2 Nova to Supernova and replace 2 Quantum Pillars with these. The impact of an early game Supernova is huge.
-Upgrade all of your cards that are key to generating the lock down which have their casting cost reduced by the upgrade: Dimensional Shield, Bone Wall, Eternity, Quintessence, Empathic Bond
-Upgrade your offense: Firefly Queen, Boneyard (optional: The casting cost goes UP but now you get 2/2 skeletons)
-Upgrade your Pillars
-Upgrade the cheap casting cost cards: Steal, Protect Artifact, Sundials
A lot of players recommended upgrading pillars first. I did this. I upgraded 6. It does not help at all. Think about it. If your first 6 "lands" are towers you get 18 RANDOM quantum. However, if you draw a Supernova, thats 24 quantum, 2 for each and this is from just a single upgraded card. In the same line of thought, if you reduce the casting cost of your shield it is easier to bring out. I'll pick a guarenteed quantum savings vs 3 random quantum any day. The first will will always help you. The latter might help and odds are it won't.
If you play this deck a bit you will realize that
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and
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are the key quantums. The upgrades that will help you most are ones that either generate these quantums or reduce cost of casting cards from those quantums.
BTW...I've been playing 2 weeks now and have 33 upgrades. It is not so hard to build an upgraded deck.