Modifying and adding things - legality?

Hello all,

I have a university project in which I have to investigate creating my university's own flavour of Firefox, which won't be used or distributed to anyone other than a specific student group. I'm quite interested in using Firefox Portable, however after some looking around it looks as if others have wanted to change things such as splash screens, and they've run into issues in terms of legality.

Could someone inform or point me in the right direction as to what sort of things one can and can't do legally, in terms of modifying FF portable, adding Flash compatibility, having addons pre-installed, etc. I'm very new to this side of things so any information is greatly appreciated.

Thanks!