Willow Shrubbery

Select your save file: For PC, these are usually in \My Documents\My Games\Borderlands\SaveData\. For the XBox 360, check out these instructions on how to extract and replace your save file using a flash drive. (credit NolaFTW) For PS3, check out this video tutorial.

These actions are taken in the order they appear here on the page. Keep a backup of your save in case this thing messes it up.

Playthrough to fix:

Glitches:

Remove glitched/viral Quests (like 'Buy Shield' and 'Talk to Tannis')
Reset any Quests/objectives that were done out of order (like knoxx armory glitches, but doesn't affect the two scaling trigger quests)

Complete playthrough (and enable next playthrough)

Complete playthrough
Complete Zombie Island
Complete Knoxx
Complete Robolution

Complete side quests

Complete side quests
Complete Zombie Island side quests
Complete Knoxx side quests
Complete Robolution Side Quests

Reset playthroughs

Reset playthrough
Reset Zombie Island
Reset Knoxx
Reset Robolution

Reset side quests

Reset side quests
Reset Zombie Island side quests
Reset Knoxx side quests
Reset Robolution Side Quests

Reset specific quests

Reset Circle of Death
Reset Circle of Slaughter
Reset Circle of Duty
Reset 'King Tossing' (King Wee Wee)
Reset 'This Bitch is Payback' (Parts 1 and 2 - Kyros, Typhon, and Ajax)
Reset 'Wanted: Dead' (Omega Assassin hit squads)
Reset Armory Quests

Advanced, Experimental, and Dangerous

Reset Playthrough 2 and enable dynamic scaling
Reset Knoxx Playthrough 2 and enable dynamic scaling
Enable all 5 Circle of Duty waves at once

Miscellany

Set save number to (0-99):

Backpack space and fixing overleveling

Set backpack space to max legit (1 for each SDU mission you've completed in both playthroughs):
or, set backpack space to slots (cannot exceed max legit value)
Balance my level for currently selected quest
Lower level by: levels under current quest