For the Pokemon Lines I would run 1 less Duskull because this is a bad pokemon to start with and it can be searched with the card I will tell you in a minute...
-1Duskull
I would also run less Warturtle just because of Rare Candy...
-1-1-0 Blastoise
You mentioned a keldeo deck before and Keldeo is always good to have in any Blastoise deck so I would definently run it...
+2 Keldeo
So Pokemon Look more like this...
3 Kyruem
2 Keldeo EX
1 Mewtwo EX
2-1-2 Dusknoir
3-1-3 Blastoise (EDIT: I love a Stage 1 in my decks for the stage 2's! Most people dont so if you do not want it, use this space to make room for the skyla which is mentioned later)
Next to the Trainer lines, and as you mentioned you are missing a few things. One your supporters are a little mixed up you definently want Cheren in this deck but not 4 and every deck must have Juniper. I love Skyla! All my decks run Skyla BUT in this deck with only 29 Trainers Skyla is less needed and currently there will be almost no space to have Skyla in it (Read EDIT) (my decks run around 35 trainers). So the supporters should be more like so...
4 N
3 Juniper (Or 4 Juniper and 2 Cheren, Your choice)
3 Cheren
EDIT: Everyone seems to say to keep Skyla after this post which I love and said before I would have so Maybe keep the Skyla and take out 1 more Energy Search and one Ultra Ball. IDK how to make room. Your Choice...
Now the items. I am not sure if you need 3 Energy Searches maybe 2 (1 Read Edit). But I know you have no Ace Spec so that is mandatory...
+1 Ace Spec (Computer Search or Gold Potion)
-1 Energy Search
Now One last card. I like to run Tool Scraper and Super Rod in my decks but you only have space for one or the other, I would pick Super Rod over any other choice but it all come sdown to your choice...
+1 Super Rod/Tool Scrapper/Switch/Other
These are all my reccomendations for this deck. None are mandatory I just want to help, I love all Dusknoir Varients and I hope this one works for you! Good luck!
Hope I Helped!