If you went the full 3" with a spacer lift up front, I can almost guarantee one of two things is happening. I've seen this before with spacer lifts, not only are they dangerous to run, but they also never fit the truck well.
Most likely what's going on, is your driver's side upper control arm is contacting the coil spring. Because of the new geometry with the spacer now pushing the strut assembly down, and essentially pulling the upper control arm in towards the truck, the inside "U" shape on the upper control arm will rub the spring. I think the rotational position of the coil is different on the passenger side, allowing the control arm to fit in a spot in between the winds of the coil, where it contacts on the drivers side.
The other thing that happens, but sounds less likely in this situation, is that when you put the swaybar back on sometimes the cradle that it sits in gets bent if you're not the gentle type when working on vehicles. This causes the bushing inside the sway bar link to "snap" against the metal cradle and make noise when the suspension articulates one way and then the other. I had this problem after installing my 5100's, and a little silicone and some massaging of the cradle fixed it.