Prepare your smoker to cook at around 225 degrees F, for about 1 hour per pound of your corned beef. You do not need to worry about drying out the pastrami, it is a dry meat anyway. The object is to cook down the meat and put some smoke flavor into it.
For wood you want something mild. While the smoke flavor is going to add to the quality of the pastrami, you do not want to over power the flavor with a strong wood like hickory or mesquite. A popular wood to use when making pastrami is maple. I also use woods like apple, cherry, or grape.
Use a heavy dose of smoke at the beginning to bathe the corned beef so it can soak in the smoke flavor.