In my playthrough for Bad ending i fought Special forces and Enforcement Squads for Good ending, however, some online guides show say that these two missions are swapped for the bad and good endings.

I only chose the Special forces craft over the Enforcement squads because it was an easier fight, its also very possible that this choice on the first playthrough doesn't matter.

Also, when choosing between Vespers or Redguns, I chose Vespers during my Bad Ending playthrough and Redguns for Good plathrough, in this case, its possible that this choice also doesn't matter.

This most likely applies to the choice given in the Attack the Dam Complex mission when given a choice, in the sense that it doesn't matter.

According to a guide i found for Good and Bad endings, only a single late Ch.5 mission choice dictates your ending

• Chapter 3 - Destroy Special Forces Craft
  
• Chapter 4 - Intercept Vespers
  
• Chapter 5 - Intercept Corporate Forces

• Chapter 3 - Mission 21: Eliminate the Enforcement Squads
  
• Chapter 4 - Mission 31: Intercept the Redguns
  
• Chapter 5 - Mission 38: Eliminate “Cinder” Carla

• Chapter 1 - Attack the Dam Complex - Refuse or Accept ( apparently both work )
  
• Chapter 3 - Prevent Corporate Salvage of New Tech

• Chapter 1 - Attack Dam Complex - Choose Accept
  
• Chapter 3 - Eliminate the Enforcement Squads

• Chapter 1 - Escort Weaponized Mining Ship
  
• Chapter 3 - Coral Export Denial
  
• Chapter 3 - Prevent Corporate Salvage of New Tech
  
• Chapter 4 - Eliminate V.III
  
• Chapter 5 - MIA
  
• Chapter 5 - Regain Control of the Xylem
  
• Chapter 5 - Coral Release

Complete Arena and Defeat last opponent