I have a major quest running and after it's finished I want the script to keep running (so I won't stop the quest), but I have a lot inside the Gamemode block and I'm wondering if I just do a condition check at the start of that block (If bFinished != 1) will the game skip past the entirety of it and waste no more time?

Why not set up a quest stage and have the Gamemode stuff stop when it reaches that point, and let the rest keep going?