The creation of a custom productivity system is a very personal process. You are choosing to skip the purchase/use of an off the shelf system, and saying that one size does not fit all. In creating a productivity system there are many choices to make, what is the planning methodology you will follow, what kind of focus do you need, are you going to use a paper, digital, or hybrid system.
Paper Systems
Some people prefer a paper system, because they feel it is easier to use, does not break down, and can be easily customized. Paper systems usually rely on a series of forms to create the system. While it is possible to create your own forms, it is a lot easier to rely on forms that have already been created. (http://www.diyplanner.com)[DIYPlanner.com] has such as set of forms, as well as a large supply of user added forms to draw upon.
The downside to a paper system is that you usually end up carrying around an extra binder, or planner in addition to what you are already carrying.
Digital Systems
Those who prefer a digital system like the idea of not carrying around anything extra. This group of people already have a smart phone, tablet, or Internet access, and wish to leverage this for their needs. When using a digital system you are at the mercy of the app designers so you may not be able to customize as much in some ways. With that said if you are one of the followers of a mainstream planning methodology you may find an app that is serviceable for you.
Building the Custom System
If you are going to build a custom system then start with a methodology. A strong methodology will help you in many ways. If your system stops working you can look at the flow of the method to help reform your system and make it better.
The second item you will need to do is to look at the type of system you want. Do you want a paper system, or do you want a digital one. Decide which tools you will use to create use, and maintain the system.
Once you know the methodology you are going to use, and the tools define how it all fits together. The end result of this will be your system.
In Conclusion
Remember that if you decide to use a methodology and it has forms, or flows already created that you can make use of what has come before. Do not feel like you have to entirely reinvent things. The goal of a planning methodology is to assist you in keeping priorities straight, and accomplishing everything you need to, and most of what you want to.