The basic method for making pastrami from scratch is to start with a mostly trimmed beef brisket. If you buy a trimmed brisket at the store or butcher it will have no layer of fat on it. For the best results, it is best to have a very thin layer of fat on your brisket to make pastrami, about 1/4 inch. This means separating the flat and the point. For those of you who don't have a lot of experience with brisket, a whole brisket is actually two pieces of meat separated by a thick layer of fat that are referred to as the flat and the point.
From this point you need to corn the beef. This is done in several different ways. The easiest and safest in my opinion is to use a brine. The salt-water brine preserves the meat and gives it the texture that we would call corned beef. The basic brine consists of water, enough salt to float an egg and seasonings like black pepper, coriander, juniper berries, garlic, etc. People who make their own pastrami usually end up with a recipe unique to them. The beef brisket should remain in the brine stored in a cold, dark place for anywhere from seven days to three weeks. You do need to regularly check on the meat and turn it to prevent spoilage.
Once you have corned beef you need to rinse the meat off. If you have brined it for a long period of time, like three weeks you might want to soak it overnight in fresh water to lift some of the salt out. Now, apply a rub and place it in a smoker. The old fashioned way of preparing pastrami is to cold smoke it. This will give it a more pastrami like texture, but not that many people have the smokehouse to do this. A modern, "hot" smoker will do the trick. Smoke your brisket for about 45 minutes to an hour per pound. Keep this part in mind when selecting a brisket. A ten-pound brisket can take 10 hours to smoke. Once the meat has reached an internal temperature of 165 degrees it is done. You do not need to smoke pastrami as long as you would a regular brisket. The long brining time will make the meat tender.
Homemade pastrami is one of those things you need to be careful with. Because you cure the meat for a long period of time the risk of spoilage is high compared with other smoked foods. Make absolutely certain that everything, including your hands, that come in contact with the meat is very clean. Make careful observations of the meat during the whole process. And make sure that every inch of the meat reaches 165 degrees before you remove it from the smoker.
Pastrami is kind of a hobby, experiment to find out what works best for you. I guarantee that once you've found your method, you won't want to buy pastrami again.