We have discussed this at some length on the Insight forum as well.
Insight Thermos Modification - Insight Central: Honda Insight Forum
I went as far as to get the special prius three way valve and pump and a stainless steel 2-3l thermos but never installed it. I added a 12v heating element into my thermos so you could boost the coolant temp with a very low current heater (even a solar panel on back shelf) as the the mod is not limited to winter use. I even knocked up few bits on the bench and bought some paraffin wax granules. i think the wax does expand a bit so you would have to leave a bit of room for that.
I think the thermos needs to be in the engine comp and hoses as short as possible, only one pump is reqd. There is a diagram of the prius system on the Insight thread.
I like the phase change fluid/wax idea and if you used a vacum bowl or wide neck flask you could incorporate a large surface area heat exchanger into it before soldering on a cover/end plate and insutalting that.
I was going to use simple pic12F683 and a couple of I2C temp sensors to monitor thermos internal temp and engine block temp and control pumping/valve with that.
Please post some pics of your setup.