Sounds like you've covered a lot of bases, so kudos to you for doing all that. What you've done makes a lot of sense. Here's what else I can think of, if it were mine.
If only ever driven at slow speeds on short trips, and with it never getting a chance to warm up, your engine might have a lot of carbon build up (you would have seen some of this in the Throttle body and the IAC, probably). I'd try some Lucas fuel treatment in several tanks of gas (or try Shell V Power gas, which has extra cleaners) to try to clean out your fuel injectors and upper cylinders. Be sure to blow out the cobwebs by accelerating quickly so your RPMs get over 4.5 or so, to dislodge those carbon deposits. Then go back to regular 87 gas after a few tanks.
In terms of spark plugs, the plain old copper cores work the best in the 3.7. I would say try those and see if it improves the idle over the fancy platinums you have in there now. (Will only set you back $12 as they are $2 each)
In terms of the vacuum lines, I think the mechanic is probably right, as the air flow would be towards the air box / throttle body where there would be less pressure due to air being sucked into the engine.
I'm assuming there is no check engine light illuminated, but it might be worth seeing if there are any pending codes in the computer for misfires. A code reader is a good tool to pick up and have on hand, or you could have an auto parts store check it for free. If a particular cylinder is misfiring, move the ignition coil for that cylinder to a different one to see if the code follows. If yes, you have a bad coil.
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2008 Liberty Sport 4x4 Automatic
Jeepin By Al 4" Lift Kit
BFG KO2’s 245/75R16
Full MOPAR skid plates
Rock Lizard Skink Super Sliders
AtTheHelm Front Recovery System & Roof RackM116A3 Trailer build thread: viewtopic.php?f=72&t=77997