• 01. Story missions are numbered and highlighted in bold text.
  
• 01. Side missions are numbered with a new list and highlighted in italic text.
  
  • 02. The further away from the left-hand margin a side mission is indicates that the mission directly above it must be completed before it becomes available.

Thanks to Borderlands Wikia[borderlands.wikia.com]

I played this game with a friend of mine in coop. I played Roland (Soldier) and he played Mordecai (Hunter). The timestamps, you'll find in this guide, is always the time, we needed together to finish all missions.

We use a shared Google Docs document, where we check all done missions like this:

• 01. Story missions are numbered and highlighted in bold text.
  
• 01. Side missions are numbered with a new list and highlighted in italic text.

Underscore means active mission, strike means done mission.

You can copy this missionflow easiely into a document and do it the same way! :)

46 main missions - 70 side missions - 10 Claptrap rescues --- 126 total missions (~25h - 30h)

• 01. Fresh Off The Bus
  
• 02. The Doctor Is In
  
• 03. Claptrap Rescue
  
• 04. Skags At The Gate
  
• 05. Fix'er Upper
  
• 06. Blinding Nine-Toes
  
• 07. Nine-Toes: Meet T.K. Baha
  
• 08. Nine-Toes: T.K.'s Food
  
• 09. Got Grenades?
  
• 10. Nine-Toes: Take Him Down
  
• 11. Nine-Toes: Time To Collect
  
• 12. Job Hunting
  
  • 01. T.K. Has More Work
    
    • 02. Why Are They Here?
      
    • 03. T.K.'s Life And Limb
      
    • 04. By The Seeds Of Your Pants
      
• 13. Catch-A-Ride
  
• 14. Bone Head's Theft
  
  • 05. Get A Little Blood On The Tires
    
• 15. The Piss Wash Hurdle
  
  • 06. Hidden Journal: The Arid Badlands
    
  • 07. Claptrap Rescue: The Lost Cave
    
  • 08. Shock Crystal Harvest
    
• 16. Return To Zed
  
• 17. Sledge: Meet Shep
  
  • 09. Braking Wind
    
  • 10. Get The Flock Outta Here
    
• 18.Sledge: The Mine Key
  
  • 11. Scavenger: Sniper Rifle
    
    • 12. The Legend Of Moe and Marley
      
    • 13. Circle Of Death: Meat And Greet
      
      • 14.Circle Of Death: Round 1
        
        • 15. Circle Of Death: Round 2
          
          • 16. Circle Of Death: Final Round
            
• 19. Sledge: To The Safe House
  
  • 17. Claptrap Rescue: Safe House
    
  • 18. Scavenger: Combat Rifle
    
  • 19. What Hit The Fan
    
• 20. Sledge: Battle For The Badlands
  
  • 20. Find Bruce McClane
    
  • 21. Product Recall
    
  • 22. Insult To Injury
    
  • 23. Schemin' That Sabotage
    
• 21. Leaving Fyrestone
  
  • 24. Big Game Hunter
    
• 22. Getting Lucky
  
• 23. Powering The Fast Travel Network
  
  • 25. Scavenger: Revolver
    
  • 26. Fuel Feud
    
  • 27. Death Race Pandora
    
  • 28. Ghosts of the Vault
    
  • 29. Well There's Your Problem Right There
    
• 24. Road Warriors: Hot Shots
  
• 25. Road Warriors: Bandit Apocalypse
  
• 26. Power To The People
  
  • 30. Claptrap Rescue: New Haven
    
  • 31. King Tossing
    
  • 32. Corrosive Crystal Harvest
    
  • 33. Claptrap Rescue: Tetanus Warren
    
  • 34. Like A Moth To Flame
    
  • 35. Is T.K. O.K.?
    
• 27. Seek Out Tannis
  
  • 36. Scooter's Used Car Parts
    
  • 37. Up To Our Ears
    
  • 38. Firepower: All Sales Are Final
    
    • 39. Firepower: Market Correction
      
      • 40. Firepower: Plight Of The Middle Man
        
      • 41. Jack's Other Eye
        
  • 42. Scavenger: Submachine Gun
    
  • 43. Hidden Journal: Rust Commons West
    
• 28. Meet 'Crazy' Earl
  
• 29. Get Off My Lawn!
  
  • 44. Today's Lesson: High Explosives
    
  • 45. Claptrap Rescue: Scrapyard
    
• 30. Hair Of The Dog
  
  • 46. Missing Persons
    
    • 47. Two Wrongs Make A Right
      
  • 48. Middle Of Nowhere No More: Investigate
    
    • 49. Middle Of Nowhere No More: Fuses? Really?
      
      • 50. Middle Of Nowhere No More: Small Favor
        
        • 51. Middle Of Nowhere No More: Scoot On Back
          
        • 52. Altar Ego: Burning Heresy
          
        • 53. Scavenger: Shotgun
          
        • 54. Hidden Journal: Rust Commons East
          
        • 55. Circle Of Slaughter: Meat and Greet
          
          • 56. Circle Of Slaughter: Round 1
            
            • 57. Circle Of Slaughter: Round 2
              
              • 58. Circle Of Slaughter: Final Round
                
• 31. The Next Piece
  
  • 59. Earl Needs Food...Badly
    
  • 60. Claptrap Rescue: Krom's Canyon
    
• 32. Jaynistown: Secret Rendezvous
  
  • 61. Relight The Beacons
    
  • 62. A Bug Problem
    
  • 63. Altar Ego: The New Religion
    
    • 64. Altar Ego: Godless Monsters
      
  • 65. Smoke Signals: Investigate Old Haven
    
    • 66. Smoke Signals: Shut Them Down
      
  • 67. Claptrap Rescue: Old Haven
    
  • 68. Bandit Treasure: Three Corpses, Three Keys
    
    • 69. Bandit Treasure: X Marks the Spot
      
  • 70. Green Thumb
    
• 33. Jaynistown: A Brother's Love
  
  • 71. Dumpster Diving For Great Justice
    
• 34. Jaynistown: Spread The Word
  
• 35. Jaynistown: Getting What's Coming To You
  
  • 72. Wanted: Fresh Fish
    
  • 73. I've Got A Sinking Feeling...
    
• 36. Jaynistown: Unintended Consequences
  
• 37. Jaynistown: Cleaning Up Your Mess
  
  • 74. Claptrap Rescue: Trash Coast
    
  • 75. Bait And Switch
    
  • 76. Earl's Best Friend
    
  • 77. House Hunting
    
• 38. Another Piece Of The Puzzle
  
• 39. Not Without My Claptrap
  
• 40. The Final Piece
  
  • 78. Claptrap Rescue: The Salt Flats
    
  • 79. Scavenger: Machine Gun
    
  • 80. Claptrap Rescue: Crimson Fastness
    
• 41. Get Some Answers
  
• 42. Find The Echo Command Console
  
• 43. Reactivate the ECHO Comm System
  
• 44. Find Steele
  
• 45. Destroy The Destroyer
  
• 46. Bring The Vault Key To Tannis

Fast travel to "Jakobs Cove".

10 main missions - 14 side missions - 1 Claptrap rescue --- 25 total missions (~ 4h)

• 01. Welcoming Committee
  
• 02. Is The Doctor In?
  
  • 01. Eggcellent Opportunity!
    
  • 02. Pumpkinhead
    
  • 03. Missing: Hank Reiss
    
  • 04. TK Lives!
    
    • 05. Brains
      
      • 06. Braaains
        
        • 07. Braaaaains
          
          • 08. Braaaaaaaaaaaains
            
            • 09. Braaaaaaaaaaaaaaaaains
              
• 03. House of the Ned
  
  • 10. Leave It To The Professionals
    
    • 11. Here We Go Again
      
• 04. There May Be Some Side Effects…
  
  • 12. It's Alive
    
  • 13. The Pack
    
• 05. Secrets and Mysteries
  
• 06. Jakobs Fodder
  
  • 14. Upsale
    
• 07. Hitching A Ride
  
  • 15. Claptrap Rescue: The Lumber Yard
    
• 08. A Bridge Too Ned
  
• 09. Night of the Living Ned
  
• 10. Ned's undead, baby, Ned's undead

Fast travel to "The Underdome"

1 misson (~ 4h)

• 1. Prove Yourself.

This mission is about competing three arenas.

If you want to get the other 4 achievements, this will last at least 15 more hours on a high level. One little trick is, to let the host play a low level char and your high level mate farms moxxi's. But this also takes 4+ hours for any of these stages.
To get the achievements, you have to do this all with one char. You'll get no XP and no weapon skills with these challanges. After defeating one, you get one skillpoint.

Fast travel to "T-Bone Junction".

15 main missions - 27 side missions - 1 Claptrap rescue - 43 total missions (~ 12h)

• 01. Scooter? But I Don't Even Know Her.
  
  • 01. Big Crimson Brother is Watching
    
  • 02. Wanted: Dead!
    
• 02. Boost the Monster
  
  • 03. Core Collection
    
• 03. Greasemonkey
  
• 04. You've Got Moxxi: Roadblock
  
• 05. You've Got Moxxi: Moxxi's Red Light
  
• 06. Prison Break: Road Warrior
  
  • 04. Road Rage
    
  • 05. Power Leech
    
  • 06. OMG APC
    
  • 07. Purple Juice!
    
    • 08. Little People, Big Experiments
      
• 07. Prison Break: Over the Wall
  
  • 09. Claptrap Rescue: Lockdown Palace
    
• 08. Prison Break: Try Not to Get Shanked
  
• 09. Rendezvous
  
  • 10. This ♥♥♥♥♥ is Payback
    
• 10. Code Breaker: Analysis
  
• 11. Code Breaker: Time is Bullets
  
• 12. Athena Set Up Us The Bomb
  
  • 11. Drifter Lifter
    
  • 12. Knoxxed Out
    
  • 13. This ♥♥♥♥♥ is Payback, pt. 2
    
  • 14. Thrown for a Loop
    
• 13. Bridging the Gap
  
  • 15. Bugged
    
  • 16. Stain Removal
    
  • 17. Lost Lewts
    
• 14. Armory Assault
  
• 15. Loot Larceny
  
  • 18. You. Will. Die.
    
  • 19. Mop Up
    
    • 20. Super-Marcus Sweep
      
      • 21. Local Trouble
        
        • 22. It's Like Christmas!
          
  • 23. Circle of Duty: New Recruit
    
    • 24. Circle of Duty: Cadet
      
      • 25. Circle of Duty: Private
        
        • 26. Circle of Duty: Corporal
          
          • 27. Circle of Duty: Sergeant
            
            • 28. Circle of Duty: Medal of Duty
              

In "You.Will.Die" you have to beat Crawmerax, a level 61+ boss. The time for leveling isn't calculated in this guide.

Fast Travel to "Tartarus Station".

7 main missions - 14 side missions --- 21 total missions (~ 8h)

• 01. Are You From These Parts?
  
  • 01. Fight For Your Right To Part-E
    
    • 02. Parts Is Parts
      
      • 03. We All Have Our Part To Play
        
        • 04. A Part Of Something Larger Than Yourself
          
• 02. New Contact
  
  • 05. Like Shootin' Rakk in a Barrel
    
  • 06. Spa Vs. Spa
    
    • 07. One-UpmanPipp
      
  • 08. Burnin’ Rubber
    
• 03. Operation Trap Claptrap Trap, Phase One
  
  • 09. It's a Trap... Clap
    
  • 10. Finger Lickin' Bad!
    
• 04. Operation Trap Claptrap Trap, Phase Two: Industrial Revolution
  
  • 11. Taking Stock
    
• 05. Operation Trap Claptrap Trap, Phase Three: TripWIRED
  
  • 12. Not My Fault
    
  • 13. Old Spicy
    
    • 14. Eleven Rakk And Spices
      
• 06. Operation Trap Claptrap Trap, Phase Four: Reboot
  
• 07. Helping is its own reward... Wait No it isn't!

The collecting achievements are funny... not! You have to farm the boss for like 8 hours or idle in a corner for about 30+ hours to collect all parts you need.

A missionflow guide to Borderlands 2 is already in work. You'll find (the link to) the guide in Jan '19.