I *think* the original 5x5 had high pulls in place of deadlifts and powercleans in place of rows. As written on madcow's geocities cite, we've got rows & deads instead for various reasons. The main thing is that you pick a squatting exercise, a pressing exercise, and a pulling exercise. Train them 3 times a week. Add weight in a consistent, logical fashion. You really should run the linear/intermediate program AS WRITTEN at least once. That said, if for some reason you CAN'T, then you can make a substitution but you NEED to select another basic free weight compound exercise. Swap a pull for another pull, a press for another press. HOWEVER, YOU CANNOT SUBSTITUTE THE BACK SQUAT!! Just squat.
Big picture: pick good, time-tested basic compound exercises that target most of your muscle mass. Work a squat, a press, a pull, each workout, and work them progressively, w/ the goal of constantly adding weight to the bar.