Hi Jon

It's hard to answer a question like this without being able to see everything in the system.

First I'd say the "overheating" does not produce any change in the sound.  The systems are self protected and in the case of overheating they would perform up until the time that the system would judt shut down to protect itself from damage.  Can you ever hear the fan operate in the main panel?  If so I don't think this is the problem.

Overdriving the system won't hurt the system but it wioll sound bad.  The position of the knob doesn't affect how hard the amp operates.  The amp always is running at 100%.  The level control just allows more or less signal into the system to be amplified.  Think of it as pinching a garden hose connected to a sprinkler.  The sprinkler always fully throws out the water it recieves but pinching the hose allows less water to get there.  So setting the input level control is a function of the output level of your mixer.  You should set your mixer to it's maximum output (pre distortion) and then turn up the speaker input control until you either get enough level for the gig or until you hit the limit LED.  If it's not loud enough at that point then you need a bigger system.  Now just run your mixer up to that point or a little below, ensuring you never exceed it.  You might also back down the input level on the speakers just a little for an extra layer of protection.

As far as "pops" they could be coming from anywhere in the system.  You "hear" them from the speakers but with the little info provided there is just no way to know the cause of them.  Most times it is coming from cables and connectors, but there's no way to know here.

The other common possibility is that you could be sending a signal that has too many very low frequencies in it and then boosting it in the mixer.  The StageScape speaker all have protection from this, but it is possible in some mixers to add too much bass EQ and begin to defeat this.  Again if this is the case then you will either need to turn down or add more subs.

Let me ask you ... was the sub flat on the floor?  How far away from the back and side walls? 

If the answer to any of these is about 4 feet then you may be getting acoustic boundary cancellation.  That can suck the lows out acoustically.  Then when you try to replace then electronically you just burn up power without getting any acoustic result.