How to determine Center of Gravity of the airplane parts?
Let’s start with a definition from Airplane Flying Handbook:


  Center of gravity (CG). 
  
  The point at which an airplane would balance if it were possible to
  suspend it at that point. It is the mass center of the airplane, or
  the theoretical point at which the entire weight of the airplane is
  assumed to be concentrated. It may be expressed in inches from the
  reference datum, or in percent of mean aerodynamic chord (MAC). The
  location depends on the distribution of weight in the airplane.


Your center of gravity calculations will start out by deciding where you want to place the datum. Typically it is placed at the firewall, but sometimes it is at the tip of the spinner.

For every piece on the airplane you measure the distance from the datum. That is called the arm. For my Cherokee the front seats are at 37 inches from the firewall. Let’s say that the seats weigh 20 lbs. The moment is 20*37=740. There are two of them, so total moment is 1480. Do this for every item on the airplane and then add them up.

Divide the total moment by the total weight to get the center of gravity.

Lots of things are fairly easy to estimate: engine, prop, battery, seats, cowl, tail have easy to calculate centers of mass.

Where it gets complicated in your case is that some of the parts of the airplane can’t be treated as residing at a point. You would need to balance them to find their individual center of gravity. Or you could break them down into parts and add up the parts. For example, you could calculate the weight the last two feet of the fuselage and use the middle of that as its ARM. Then the next two feet, etc. Same with the wings.

If you are using standard parts there may already be CG information from other builders or the supplier.

This will give you an idea as to where the CG is but when you are done you need to weight the airplane and calculate the true CG. This article goes into detail on the method and calculations.