Unable to start engine on 2007 Nitro-no clicking from starter-opened hood and found clicking noises from breakers in box next to battery...removed 3 large gray square ones to stop clicking sound A second clicking sound was coming from beneath the air hose between the firewall and the air intake cover on top center of engine. I removed the + cable to reset "the brains" and went to test the battery and found it 95% charged. Anyone have a clue?

Tell us the year, make, model

I don’t think the problem is associated with replacing the water pump - the clicking noise is the solenoid on the starter motor not holding in - the Solinoid is either faulty or the battery is too flat to keep it engaged.
Check the battery voltage while it is clicking - or charge the battery - if the problem persists you could pull the starter and get it checked by an auto electrician.

Where's the clicking noise coming from ? Under the dash , under the hood in the engine compartment ? Do starter circuit voltage drop test ! When the key is in start position is there constant B+ voltage at the 10 amp crank fuse in the under hood fuse box ? This is an input to the PCM - engine computer to energize the starter relay ! Starter Voltage Drop The battery is good , starter is new ,what about the cables ? watch this video on testing starter circuit !

Sounds like the solenoid on the starter is not getting any power, check the small wire connection on the starter to see if there is power in the start position, if not you have an ignition switch problem or an open circuit between the ignition switch and starter solenoid... if you do have power in the crank position then you have a bad starter.

On the fuse box lid should be diagram of relay positions , The relay that's clicking ,what's it for ?

Check your Negative cable attatched to your starter. Next check your charge on your battery, a clicking noise indicates one of 2 things, 1. your battery is dead or dying and needs to be replaced, a battery charge will only solve the problem temporarily, it will continue to die and ruin your alternator. 2. your starter solenoid is going bad, being unable to deliver enough juice to your copper terminals surrounding the magnet that pushes the small gear pinion on to the flywheel and turns the motor to start.

If even with a new battery the starter doesn't turn the engine then it's the starter the one that has died, taking the battery with it. You will gonna have to remove it from the car and test it - if it fails don't try to fix it (the parts themselves will cost you more than a refurbished one), just replace it.

asd/ignition relay shorting or possble pcm/gem failure. Depending on mileage, I would return to dealer as this is a warranty issue.

Well if your battery is ok than you more than likely need a starter.

Is the clicking sound from under the dash or under the hood? Does the engine crank over?