If you're lifted re-tighten every single bracket nut and bolt that was put in place for your lift, and a few that were factory (transmission crossmember, motor mounts/brackets, pivot arm if using bolts, etc). I have to tighten my bolts to spec with a torque wrench every so often. Also recheck things like your u-bolt nuts as they tend to loosen quite a bit, it can take months of tightening them before they stay to spec. I had the exact same popping and clunking, specifically it was the pivot arm brackets that were to blame for me, now I just retighten them every few months.
When you replace factory rivets with bolts, per Ford's instructions, you're suppose to tack-weld the nut in the end, they also call for ridiculously high torque for the bolts, twice what most lift-kit manufacturers call for.
edit: there is also a TSB for the transmission cross-member and for the factory frame rivets. For the tranny cross member, look up the TSB, it really helps your chassis feel better after it's done. The TSB for the rivets calls for drilling them out and then putting nuts and bolts in their place, it's a huge PITA so hope that you're not dealing with loose rivets.
It's also common to crack your frame near your steering box, this will cause popping and creaking. It's hard to notice the crack, have someone turn your wheel and check for excessive flex in your front left section of frame, this might also point to loose rivets near the steering box as well, which are pretty darn common.