Might sound overkill, but if you are having trouble keeping track of story plots etc
I use Notepad++ to write the story / plan for a quest , system etc
Its a practice I started doing, mirroring what we do in work. (Product Development for a Software firm)
Its a somewhat loose adaptation of Agile.
BA (Business Analysts)
Developers
QA (Quality Analysts)
We all get together, discuss upcoming features, and write down 'stories' for the features.
Eg:
A BA may have given us a broad topic/feature such as.
As a Customer
I should be able to get my Login Credentials when forgotten
So I can continue to use the awesome web site.
Putting this in context for a creative story.
As a player
When I beat the boss of level 5
My character will be granted the ability to teleport to his stronghold.
So this is a broad topic: What our player (customer) is going to want to achieve.
You might think that this has no value what so ever, but believe it or not, sometimes these generic phrases when looked back on, can help you identify when you have gone off on a tangent and your plan has gone off course. So they serve a function to keep you on the right track.
So As a builder/scripter you could then break this down into other tasks
As a builder
* Must create Level 5
Use Dungeon Tileset
Enemy group will be Wolfmen
* Must Create Boss
Will be named 'Garog the Blind'
Will have claw weapons that deal high damage proportional to his own health levels (Scripting task)
On Death - Set variable 'PC_KILLED_LVL_5_BOSS' = 1
As a scripter
* Must create script for claw weapons: Deal 2d12 Damage + 5% Missing health; (Attacks grow stronger closer to death)
Attach to claw weapons
* Create Death Script for Boss : PC_KILLED_LVL_5_BOSS = 1
* Prevent Player from re-doing the quest, by checking for the PC_KILLED_LVL_5_BOSS variable.
* Develop the teleport power - See task TELEPORT_01 (Might need a task of its own)
* Award the player teleport power (TELEPORT_01)
I once worked in a project management tool called redmine - which looked very promising for managing a PWServer.
You could create your project, list all the subtasks for the project, assign them to other users/people in your staff/project.
You could then check each item off on the list.
Project management tools such as redmine, Jira and maybe even mantis etc : They will also allow you to move these tasks into various states.
Such as peer review, rejected, in-progress etc.
As far as the variable tracking goes - I recommend keeping it stored somewhere in relation to your project -> quest -> feature layout.
That way you can find all variables related to a specific questline, or even search for the variable, to find out what function it serves.
So using the above structure -
the Builder will not have finished his job until his 2 tasks are complete - using the specifications provided.
the Scripter will not have finished his job until his 5 tasks are complete - using the specifications provided. (he might need to wait for the builder to make the claw weapons though)
The feature/deliverable wont be finished, until everyone has completed their tasks.