I agree with placing the filters on the pull side, since that is what all hvac units do and what the filters are designed for. To be effective, you are also corrected that a deeper pleated filter with more surface area is the only way to go. But I am unconvinced the motor will heat up. Certainly there will be less air so if it is air cooled it will heat up from that, but at the same time, a fan in a partial vacuum uses less energy and should heat up less. Just slap a meter on it and you will see the draw can be significantly lower, since it is doing less work.