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
and
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.