Designing a profile form for profiles in Quota X, and a different form for profiles in Quota Y
Using Jamroom
If you try some of these things out using the Form Designer you will be able to figure it out in much less time than it takes you to formulate your lists of questions. Most of these tasks are really quite straightforward when you try to action them. Overthinking things will just waste your time.
Try things out. You should then be able to focus your questions on your actual needs, and make it possible for someone to answer helpfully. Try things out on a test site and you will gain perspective and save yourself a lot of time.
As far as your users go, I have found that academic-type users (I think that's your market) really appreciate simplicity in a quota structure. They don't have anywhere near enough time to learn new stuff in order to make use of a good tool. They will deliberately avoid anything which requires them to spend time figuring out if their time investment is worth it or not. Keep your quota structure simple and flexible at the start, then reorganise it when practical branchings become clear.
To that end, for point 5 above, give them the same sub and help text. e.g. "Users on a Members account get 2 links but members on a Pro account get 3 links.
That text also tells them that they should upgrade in order to gain better features. They will get that, they aren't stupid, just afraid of losing a lot of time that they don't have.