Tires.... I have 225/70-15's and they work fine.... Some people said that 235/75 fit and some don't, I guess it depends on how agressive the treads are.
Roof rack.... I don't know of any company that makes them for the 99+ 2dr.... Maybe check into how they made the 89-98 2dr's and make your own?
Lockable storage...... Was an option on them.... I had one, all it is is a 3 sided(with a top) plastic bin that screws to the floor and when you close the tailgate it becomes a box that you can't get into it. Ok idea but not the greatest for useable trunk space. You also have to take the top off to get it out, so it's not something you want to do often.