I wouldn't sister the joists. YOu could easily transfer the problem 'in' your current joist to your new joists. Again, treat the existing joists and leave about an inch between it and the new one(s).
It's a good idea that if you think the problem is bigger than it is, then it is, and it's good you're gonna have a structural engineer look at it. Whether you hvae a case or not, the $$$ spent on the engineer is $$$ well spent!
If you get a chance, I'd personally be interested in hearing what he says. (My direct e-mail is everywhere on the board.) My best to ya and hope all goes well.