Terminology Bert?
Clean PWM power means what exactly? I googled it and it says pulse width modulation - which sounds complex!
http://www.tetech.com/FAQ-Technical-Information.html#19
Would it just be better to have a simple on / off switch to the peltier and attach it to regulated, always on direct current so it trys to cool its target as much as it can (rather than have a cut off thermo switch)?
A Thermostat will kill the Peltier - means don't have a current limiter based on some temperature sensing device?
Could you please explain in laymens terms what exactly you mean to tell us non electricans!
Also could you post a few picks of your coolers and what they are able to achieve - would be very instructive!