Bryan,

My best guess for the tube in the core is to pick up oil that may accumulate
in the core when used for air conditioning.  Since in the auto installation
the tubes are both at the top, it needs a way to return oil to the
compressor.

I'm not sure what the original purpose was, but on one end there was a tube
going down to about an inch or so off of the bottom.  On the other end,
there is a plate blocking off that tank about 2" down.  My guess was that
the tube pushed the liquid to the bottom of the core, and the plate on the
other end ensured that it flowed out of the top ?  Just guessing.

It sounds more to me that you may have air trapped in the cores (did you
bleed the cores?) or possibly cavitation at the pump.

The cores are probably 18 inches below the engine/pump, and 24" below the
header tank.  I can't imagine any air in there.  There was air in the pump
originally, and I had a heck of a time getting it all out.  I think (hope)
it is all out now.  After shut down, I was hearing air perk up through the
header tank.  The last run I made there was no more perking gurgling, or
other such noises.  The coolant, however, is not flowing through the entire
core.  Just the top.

Steve