Some thoughts on what happened with the MOPA cooling. 

Some unknown thing happened to precipitate the initial needle valve jiggle, which unleashed a torrent of flow through the NPRO.  This flow was made possible by the fact that the cooling lines are labeled confusingly, and so flow was going backwards through the needle valve, which was thus powerless to restrict it.  The NPRO got extremely cold, and most of the chiller's cooling power was being used to unnecessarily cool the NPRO.  So, the PA was not getting cooled enough.  At this, point, reversing the flow probably would have solved everything.  Instead, we turned off the chiller and thus discovered the flaky start-motor capacitor. 

Now we have much more information, flow meters in the NPRO and main cooling lines, a brand-new, functioning needle valve, a better understanding of the chiller/MOPA settings necessary for operation, and the knowledge of what happens when you install a needle valve backwards.