I post this because I wish someone had posted it telling me.
You all know how you acquire these upgrades if you actually play the game because it tells you before they even show up... but look for the "Strong Arm symbol"... so just keep your eyes out and consume them, nothing really strategical to do or waste time with they just show up.
This can easy be done through multiple playthroughs (with newgame+ ) so do not get to worried about it. Play the game as you would doing everything and if you do not get it your first playthrough you will easily get whats left in the second playthrough in newgame+ mode. Even if you play this on hard your first playthrough I think its still more fun and easier/faster to just start a newgame+ (because you will have to just to fully upgrade Heller anyway) to finish off any you may have missed instead of reloading checkpoints over & over & over or searching in red zone (boring).. Just play the game and enjoy it instead of getting worried about these upgrades. :)
I was missing 7 or 8 upgrades at the end of my first playthrough (easy), I stuck to the main story on my second playthrough (hard) and had them all before leaving the first zone (yellow).