Can't engineer queenside play for Black INTRODUCTION:

Recently, I have played online blitz game against very strong GM ( who is also a chess writer ). I didn't even know it until asking him if he has any ELO / title. 

We played 7 games and I lost all of them. Although I know my opening choice for White is "idiotic" I just couldn't resist and "went Sparta on him" -> sadly, he dispatched me with ease. Still, with Black, I offered real resistance. Even he said that he had to "work for those wins." 

I knew exactly when I made the mistake in all the 7 games, but for the life of me, I was not able to find an idea on how to generate long-term counterplay. 

Even analysis with StockFish 5 confirmed my evaluations but the engine couldn't find any move that will give me counter-play when I was Black. 

It also confirmed that the GM played the only winning moves which confirms that his above comment wasn't an "empty" compliment but the truth.

I am interested in improving the 3...Qd8 line of the Scandinavian defense so I will limit my question to the positions that arose from those games. 

RELEVANT INFORMATION:

To further help you, I will quote the opening positions from those games, and will give additional info / instructions in order to make your task easier.

[Title "How can Black generate counterplay?"]
[fen ""]

1.e4 d5 2.exd5 Qxd5 3.Nc3 Qd8 4.d4 c6 5.Nf3 Bf5 6.Nh4! Bg6 7.g3! e6 8.Bg2 Be7 9.Nxg6 hxg6 10.O-O Nf6 11.Ne2! ( 11.a3 a5! $8 ) 11...Nbd7 12.a4 O-O?! ( 12...a5! $8 ) 13.a5! $16


The point of Ne2! and a5! is in grabbing as much space as possible in the center ( with subsequent c4 ) and queenside. He also tried with a3 instead of a4 in other games, but the idea was the same: Ne2 -> c4 -> gain space on the queenside. 

His Bg2 killed my ...c5 push, so I was without any counterplay. I still think Black would be fine if he had played 12...a5!, but I don't see how to generate freeing break or any other sort of counterplay. 

As a good chess writer he knew for Nh4 + Nxg6 + g3! plan from the Slav defense, but so did I. It didn't surprise me. His Ne2! maneuver didn't surprise me either but the idea to gain space on queenside threw me off.

QUESTION:

How can Black generate queenside counterplay that gives him equality?

Please avoid computer-only analysis. This is the position where they can do little as it involves planning, for which engines are not capable of.
I was not able to find an idea on how to generate long-term counterplay.
How can Black generate queenside counterplay that gives him equality?

It might be cruel for you but...answer is simple: in this position black can not achieve equality or counterplay at all. Your opening choice made you wait for him to kill you or if he's not able to (can't find as you said 'best moves'), then it might end in a draw. Scandinavian is not a good choice in case of counterplay.
Let's have a look at the position without using any engines:
White adventages:

Space
Pair of bishops
Pawn structure

Black has no pluses in this position at all. If you are standing worse you want to simplify the position by exchanging some pieces. However, looking at the black's pawn structure, it might be a bad idea to go for an endgame with doubled pawns which make the majority less effective and more vulnerable.
As you mentioned before, 12. ... - a5 might have been better than 12. ...-O-O. I would rather play a5 myself. Once he got to a5 square he might want to play a6 and create weakness n c6 making his Bg2 even stronger. And you can't really play a6 yourself leaving a nice hole on b6 and making b7 pawn vulnerable for rest of the game.
Another thing is, I don't understand why you'd like to play on a queenside when you are 3-4 in terms of pawns there. Any b-pawn or c-pawn move there makes his white-squared bishop a monster.
To sum up, I'm against that Scandinavian. Reason is simple: If there's a skill gap between you and your opponent, you end up in a (bit) worse, positional position, sooner or later you will get crushed. You have much better chances to play, as you called, sparta. There's better chance in complicated tactical positions against GM than playing against his positional (and overall chess) understanding and huge experience. Scandinavian is praying for a draw for me.