Inspect the housing of the strainer, not just the cup! I had this crack one winter that I forgot to drain the strainer. I replaced the cup but still had water suction issues. Inspected further and found this. Once replaced I had no issues. 
 

Before taking it to the dealer I would also buy a gallon of coolant and check to see if you can refill, run for a bit and refill again. There is probably air in the system. I also had a leak from the coolant cap at @csleaver mentioned that caused low coolant. Never got an over heating alarm but had a lot of fluctuation. I ended up adding an entire gallon of coolant over a few fill ups & runs. 

When going back for the second time and removing it successfully, what kind of wrenches did you use and where did you place them? I can find anywhere good to hold the fitting pipe without damaging it by too much grasp force.

The RC cover goes over the module that is in the port rear compartment. Might not have been snapped on all the way.

26 minutes ago, WetSoundsTech said:

unfortanilty that would be a question for Malibu our OEM equipment interacts with their Touch screen.

Our dealer has been in contact with you all.  They stated that Malibu has de-featured all newer models to not have a proper EQ.  This stinks....

What would the new price have been back in 2001? I think my 2006 VLX was under $60.000. I sold it for $32,000 in 2014.