1. That is true, it can make it tricky to figure out which levels should be directed to brick banking and no brick banking. For those who don't know what special assignments have the required super builds, they are:

Miner Altercation, Kung Fool, Dirty Work, Colossal Fossil Hustle, and High Steal.

2. I think for the runners who want to do IL runs on a 100% file, state in the rules "You must collect the required bricks as if you entered the level with no Super bricks" and "You may use as many super bricks as you need to complete the assignment" for Story (No BB) and Story (BB) respectively. Changing the category names to more reflect the game may reduce some the confusion.

3. I think the brick amount should be what it would be if you were still trying to progress through the main story-line in the Story IL categories.

I plan on doing IL runs along with the Free Play RTA category, both of which for the WiiU.

Trajan, the best way to get in contact with the mods for this game is the join the LEGO speedrunning discord. The link to join is in the forums. That is where a lot of discussion happens between most of us in the LEGO speedrunning community as well.