Hey Ben,
IMHO thermocouples (whatever type) are good for applications that don't require high accuracy. Even with a quality TC and calibrated instrument you won't be able to do much better than about +/-0.5 deg C. TCs big advantages are they are inexpensive and widely used throughout industry (available in all shapes and sizes). If you need better precision and accuracy then 4-wire platinum RTDs are the next step up. They are more expensive but in a best case situation can provide +/- 0.01 deg C accuracy.
So I recommend looking at RTDs for the die temp and water inlet. Don't even bother with TCs. Even with good RTDs installed on the inlet and outlet of the block, I doubt we will be able to measure the Delta T across the block accurately enough enough to define the actual heatflow. To define Q based on mass flow rate and Delta T would require even more accurate (0.001?) temp readings and very accurate (0.1?) flow rates.
In regards to calculating the thermal die secondary losses - my plan is to...
1) insulate the block quite well (thermal stand-offs, air gaps and ceramic insulation) to help minimize secondary losses as much as possible.
2) Measure the secondary losses by firing up the die and applying just enough power to bring it up to a typical steady-state operating temperature (i.e. 40 C) at a known and controlled amb air temp (with the die surface insulated). Once the die equillabrates at temp, virtually all of the power going in (E x I) is going out via secondary heat paths (since there is no WB sucking heat out the top). Since I'm not far enough along to have actually done this I don't know how well it will work.
Well, so much for lunch...
