Hi,
How do you plan to isolate it? Since the input voltage is 12v, the microcontroller and MOSFET will have to have same ground. If you try to isolate it, you'll need to make an auxiliary isolated power supply, and it's not worth the hassle. Plus, the output is only 36v, so, isolation is not required. Boost topology, is, by nature, non-isolated, so it can stay like that. You can use TLP250, but nothing much to be gained.
You can use either pin, but I would take connection from pin 6. For boost converter, you have to use an ultrafast diode or a schottky diode. What is your required output current? This will determine which diode you need to use. You can't use a standard diode such as the 1N540x as they have too high a reverse recovery time.
Hope this helps.
Tahmid.