This sounds like a great idea for us n00bs out there...
Without even a sensor I could tell you that going from that 900Mhz (OCed to 1.1Ghz) Celeron to a P4 2.66 Ghz (OCed to 3.00Ghz) has REALLY raised my water temps.
The water itself feels warm to me. Not hot... but warm.
My suggestions...
As for flow through the system. I think that just about anyone could get a couple of 5 gallon (minimum) paint buckets and do the flow with that. It should be fairly accurate.
The height of the tubing to get over the top of the bucket should cancel each other out if the middle both buckets are the same height from their connection to the system.
You could also "approximate" the physical layout of your system on the bench for the flow test by simply putting boxes under each item so it's the same height from the pump as it would be in your system.
After the system is installed...
I think just about anyone (if they have it) can use a room thermometer and their old HSF setup for reference and MBM5 for the CPU measurements with something like SETI or Folding@Home running to push the CPU to 100%. (my F@H runs 24/7) I think that as long as the same "load" application used before and after, then it should be okay.
As for time to stabilize the temps... I would say let the load application run for about an hour.
Not super accurate... but it would be adequate for most people.