Engine heat under the hood, if you're water temp reads normal, I would NOT be too concerned. Yes, I suspect how crowded it is under the hood is the cause for the additional heat under the hood. More room means air circulation while moving and cooling down of the engine compartment. The splash guard on the bottom of the Commander probably reduces that air circulation to cool off the engine bay as well.
Engine tic's are pretty difficult to, if you can hear it in the passenger compartment with the windows closed, then likely it is normal.
Its hard to diagnose the source, if all you've got to go on, it tics like most Hemi's but a little louder.
And yes, charging AC with just a can and tube from the store is a risk. There are a dozen things that can go wrong to make the AC NOT work, only one of them is a slow leak that a blind charging without the right tools might "improve" NOT really fix. You need to put a set of gauges on the AC system and read the pressures, to start to understand what is going on in the AC system.