Kasuto

Well instead to talk about Invisible Stalker in specific let me talk about creatures in general, in my opinion a Mill deck shouldn't have too many creatures (at least you're playing playing Millfolk, plus i prefer to play Mill with some control) because your goal is to Mill not to kill, but right now with the addition of Wight of Precinct Six and the Cipher mechanic it's actually not that bad but... the thing with Wight of Precinct Six is that if you are playing versus a control deck you are not gonna get too much advantage from it, so Wight of Precinct Six it's it's good at 2-3 i think you should make this decision this depend on your meta-game.

If i where gonna do the changes in this deck i would cut the creature base to 12 maximum.
-1 Wight of Precinct Six (or -2 if you don't wanna take out 1 Jace's Phantasm or if your playing versus a deck with no big creature base)
-1 Invisible Stalker
-1 Jace's Phantasm
+2-3 Thought Scour (Instant - Mill 2 and you draw a card for 1 Blue... PROFIT!!!)
or
+1 Surgical Extraction (I can't describe how much i like this card, for me this is almost the perfect card for a Mill deck, you get to remove the remaining copies of a specific card you want to get rid of, it give you knowledge about the hand of your opponent and you get to see what's left on the library of your opponent, plus it's cost just 1 black mana and if you don't have the mana and you want to use right away you can pay 2 life, it's just amazing, i use this card in almost every black deck or decks with splash black)

Now to talk about other card that i would like to change is Dimir Keyrune, has i have tell it before this deck don't need a lot of mana fixing, take out those 2 Dimir Keyrune you have left and add 1-2x Jace, Memory Adept or 1x Surgical Extraction (If your decide just to add 1x Jace, Memory Adept, get the set of 4x Surgical Extraction 2 main and 2 in the sideboard they are gonna help you a lot versus control and combo decks).
Another thing that i have tell it before is to go with 2x Sleep and 2x Ætherize, believe me Sleep followed by a Ætherize can be devastation versus some decks.

If you have another questions or if you want my opinion about other things tell me i will try to help you.

Just take in count the following things i have to say if you really want to change a big portion of your deck, otherwise you can just skip this comment.

First: Please reduce the number of cards down to 60.
Now with this said i honestly think that in order to make this deck better, you should remove from this deck 3 cards and those cards are Lazav, Dimir Mastermind, Hands of Binding and Trepanation Blade.

Lazav it's a good card and have a relative good synergy with mill but... he's not made for this kind deck, what you want is to mill your opponent has soon has possible or kill him with 1 or 2 attacks from Wight of Precinct Six .

Hands of Binding again another good card but it's not made for this deck, you are already running 3x Ætherize (you should run 4 or run 2x Ætherize and 2x Sleep) on top of that the creatures you are gonna use to attack (Invisible Stalker, Jace's Phantasm and Wight of Precinct Six) already have evasion or you can give it to them via Rogue's Passage, so you don't need Hands of Binding. Plus if you really wanna be annoying you can use Archaeomancer to get Ætherize (or Sleep) back and recast it again.

Trepanation Blade: you don't need equips in this deck plus this card is too slow for this deck, for 5 mana you could cast a Consuming Aberration and get more profit from that or cast 2 Mind Sculpt and 1 Jace's Phantasm and just with that you get rid of 14 cards and get a 5/5 Flyer, once again Trepanation Blade is just too slow.

Now lets say that you decide to reduce the deck to a 60 card one, what are you gonna take out/change?

First you take out the 4x Hands of Binding and x2 Lazav you end up with 60 cards.
Now you change 3x Trepanation Blade and x2 Dimir Keyrune for 4x Mind Sculpt and x1 Ætherize.
To be honest i think you don't need Dimir Keyrune at all in this deck, you are running 25 lands and 8 of those can produce blue and black plus you are not running cards that are heavy in a specific color anyway so you don't really need alot of mana fixing.
These are the basic changes that i would do to this deck if you want me to expand in what you can change in this deck i need to know if you are building this in a budge.

Anyway i apologize for this wall of text but i really like Mill decks and i wanted to give you a hand, good luck.