Comments to original post and other comments:
1. if you have not already done so read Sir Sam's NOOB guide
2. clunk could be motor mounts or maybe bad alternator clutch. For the latter crank up and at idle look down the serpentine belt (may have to remove plastic engine cover) to the serp belt idler; if it's bouncing as opposed to barely twitching the alternator pulley is bad as needs attention ASAP. If so don't go cheap with get a new clutch from like ID parts although pulling it off can be an issue or see if you can score a lifetime warranty replacement alternator from like Autozone
3. see owners manual on when AC compressor runs. If you don't know if you have an owners manual check the shelf in the top of the glove box or download an "e" copy for the Jeep site or Sir Sam's. That feature can be disabled but as noted having the AC run some in the cold season circulates AC system lube with is good for the seals.
4. MAP sensor won't clean perfectly but as long as you can see color on the bulb it's clean enough.
5. pumping primer won't remove air unless you crack bleeder screw. See how to video on NOOB site which also shows replacement filter head which you obviously need. FYI new head comes with new filter installed.
6. sounds like your Italian tuneup took care of stumble.
7. full time light is almost certainly the switch as noted.
8. GDE Ecotune will give you the most mpg bang for the buck and will largely take care of EGR induced problems. That tune ups power and will handle towing upto and probably above 2,000 lbs just fine (based on tow from Tempe AZ to Tallahassee) without stressing the post F-37 torque convertor. "Hotter" tunes are fine but stress the TC IMHO.
9. GDE tunes shut off the viscous heater at a lower temp than stock tune or you can pull the viscous heater relay and turn it off entirely. The VH consists of an electric clutch that is triggered by coolant temp, a bearing, and internal friction stuff that when the clutch engages is designed to provide a bit of cabin heat sooner than the engine warm up cycle will. With the relay pulled the clutch stays disengaged, the bearing spins, and the internal stuff does nothing. The only downside is slower, but not much, cabin heat. In fact if you live in colder areas use of the plug in block heater will do more for cabin and coolant temp warm up than the VH will ever do. If my VH ever died I'd simply bypass it with the coolant hoses and replace the external bearing if need be (there is a how to post out there) which essentially converts it to an idler pulley.
10. I see you have an 05 so you might want to put a Hayden fan clutch on your list to replace the weak OEM fan clutch. Cost ca. $50 and a not to difficult DIY project which can be combined with a fan shroud mod to make future access easier. See
http://www.beesvillebeefarm.com/jeep.html and
viewtopic.php?f=98&t=64278&p=709322#p709322 respectively.