I plan to fill the gap between the fan and the shroud with eather foam or some other suitable material.

There is no dissadvantage to using the oem temp sensor. The Spal controller uses the OBDII sensor, and it has controlls so you can set the tempature where the fan comes on at 50% speed and the high point where it increases to 100% speed. The Spall also allows you to controll a second fan when it switches to hi-speed.

The Spal controller also has a sens lead for inginition, and with the AC sens input connected the fan runs a 100% when the AC is operating.