Hmmm......
Clunking sound? As suggested pull your valve covers to determine if a rocker arm has come out from under one of the cams. This can make a noise if the rocker arm flops around in the valve cover and then make the engine act like it skipped timing. Rocker arm tensioners can leak down and allow too much clearance under the cam allowing the rocker arm to come out of position. If this has happened, replace the tensioner. Check you tube for videos on rocker arms on Libertys and 4.7l Dodge V8's
Charging circuit low? After getting the engine started, I would pull the fuse and relay to the coolant fan circuit to see if the low voltage problem goes away. The coolant fan circuit may well have a short causing the voltage to drop. Check the fan motor and relay for internal shorts. I had a similar problem with the fog light switch on a PT cruiser which drained the battery. Replaced the multi function switch (includes fog light switch) on the steering column and battery/charging problem went away. Replacing an 07 battery is good - 8 years on a battery was good life.
let us know how this works out.