If you haven't replaced you PCV valve in the last 30,000 miles it's probobly time to do so.
Bad Postive Cranckcase Valve commonly has valvetrain noise and excessive oil consumption.
If your JK is making noise at startup your oil filter may not have a good anti-drainback valve.
The butterfly valve on your intake manifold may be dirty as well.
Carb cleaner and rag is all it takes.
Remove tube between air filter and intake manifold at the intake side and clean the flapper off real well.
If your engine stubles at idle replace your spark plugs.
Good news is even if all of these things need fixing your only looking at about $60 in parts and an hour or two of shop labor at most.