Get yourself a 6-8' straight edge, and then hold it across several of your joists. Better yet, even, just string a line across all of them from one end of the room to the other.
If you can live with actually seeing all that variation in your panels, use that system.
I suppose you could just shim all the high ones to equal the low ones, but you've got to ask yourself: 'Am I feeling lucky?'
Think about it before you do it.
As far as needing 4" for a normal dropped ceiling: You can get by with 1" if you're willing to remove a cross bar to slide the first row of panels into place, and then put it back, then do another and so on.
Best of luck.