Before you jump into a building a custom motorcycle project there are a few things you'll need to look at. Building a bike from scratch is a lot different than just customizing a stock motorcycle where you can be sure that all the parts will fit. You can not just start buying parts willy nilly and expect them to go together. Here's a checklist of things you need to do before buying anything.
1. Make a decision about what engine you plan on using. Your engine decision is critical to other aspects of the build such as frame compatibility, transmission, charging system and carburetor requirements. Buying or using a factory engine will make doing future service work much easier than grabbing some fancy large bore aftermarket engine.
2. Decide what size rear tire you are using. Again, another issue that determinates other items such as wheel choice, frame usage and fender selection. Tire width impacts handling and an overly wide tire will force you to use an offset transmission. You need to know all these things before you buy a frame.
3. Determined desired rake on frame neck. This is not always easy. Varying your rake also varies your front end height, proper length of your forks and is relative to front wheel height also. For an absolute beginner my suggestion here would be to find a bike you like and find out exactly what the rake, front wheel size and fork tube lengths are. Also find out how much trail that bike has as this is a key for handling. Just because a bike looks cools does not mean it's rideable. You can find frames that give the appearance of a longer and raked out front end but actually use factory dimensions. The look is achieved by pushing the steering neck a little forward and sweeping the down tubes back in a sharper than normal angle.
Once you have one custom bike under your belt, you can start to come up with your own plan. If you happen to be able to use a graphic design program such as AutoCAD you can actually design various rakes, heights and front end lengths to see what kind of trail they will give you. This may be the most critical decision in the whole process. If you make a bad decision on the front end it will affect the handling, the look and the overall height of the bike. First time out copy another bike.
4. Make a realistic list of things you will be capable of doing and things you will need to farm out, such as painting and electrical. Attempting things that are way over your head could make you end up putting this build off to the side for long periods of time. Most people can handle general assembly of parts but run into difficulties when it comes to electrical needs. Many project bikes are sold still requiring the electrical work done. Often the only thing that needs done. Plan on having someone else do it if it's not your field of expertise. Same goes with painting and especially welding. As complete as your frame may be something always looks to need welded. Plan on what you're going to call to do it.
5. Budget for tools and miscellaneous items you do not already have. Simple things like placing seals in fork tubes will go so much smoother with the proper tools. You can not assemble a bike with a set of wrenches and a hammer and there will be connectors and such you forget to buy. Always assume up to a 10% overrun on your original budget. Plan on buying additional tools as you need them, do not try an anticipate everything you will need as some tools are highly specialized and you might make a bad purchase and end up with an expensive tool .. And buy a lift, you will never regret it.
There will be a lot more decisions you will need to make as you go such as selection of lights, mirrors, wheels and tires but if you get these 5 things determined before you begin your project your custom bike building experience will go a lot smoother. Always plan ahead for your engine, frame, front end and wheels and find all the compatible items including your rear fender before you buy any of them. You should be flexible on most items after that as items like gas tanks, oil tanks, front fenders, seats and lighting are usually available or adaptable to anything you already have. Best of luck.