The clicking... If you can feel it in the floor, that makes me think it's something "heavy" as a ujoint will typically click under coast but not load and perhaps give you vibes as well while under load. But other than vibrations it's not typically likely to be felt in the floor, especially if the ujoints passed your visual check.
If the other issues like timatoe mention check out and that doesn't fix it, look at your spring bushings. I can't see the specs on your jeep, but since you have an SYE and mention a 3" lift (I assume spring lift?) and installing the SYE I assume the springs and bushings are new. But give them a look-see cuz you can and it's free. If you have a 3" body lift, however, that's a lot of potential for noise/movement because of the leverage provided by the height- though again an SYE suggests a spring lift since it's not required for a body lift.
Then check out your rear axle ubolts and centering bolt for the springs. With the length of some axle spring mounts, once the springs settle in, there's a potential for movement and hence noise.
Other things that make noise are the front sway bay bushings, link bushings, body mounts, and the track bar. The front end lifts when power is applied and dives on let-off and braking and something loose will make a noise. I mention the track bars because if your jeep is from the north the bushings could be beat out or more likely frozen solid. You *might* need track bars for state safety inspection in your area; dunno. But removing them will improve your ride comfort substantially. Even though I knew the track bars were not really needed and removing them could improve my ride quality, when I did it it was an eye opener. Mine were frozen motionless. Amazing improvement, and it let my jeep show me the spring bushings were bad. Replaced those and my road wander stopped, too.
Then there's mechanical stuff. A worn out ring and pinion, excessive side play in the ring gear, or an early warning of a pinion bearing failure can be culprits.
After that or maybe right away I'd look into the motor mounts, too. It's hard to make them show you a problem in the driveway cuz it's just little you compared to all the weight and torque of the whole jeep pulling on them.
I'm just trying tho think through what could possibly be the source of a single click you can feel in the floor boards. If you still have the D35 rear axle, though, if I had to guess at something "heavy" I'd point there. But the other checks are free and will take under an hour and maybe they will reveal something. I'd hope for a simple fix for you rather than a differential issue.
shackles or D rings?
wrong words brake the web
cranking IS turning over