Like all complex artifacts, aircraft primary structure design is an iterative process. It begins with aerodynamicists designing the Master Surfaces of the Aerodynamic Envelope. Structures designers then cope with the space requirements thereafter, although compromises between multiple design teams will often be needed.
A few things will be known. We will know the intended operating envelope of the aircraft with some intended design limitations in airspeed, maximum Mach no., service ceiling, etc of the aircraft so we can calculate the aerodynamic loads on the pylon. We also can obtain performance numbers on the engine, so we can determine the thrust loads and moments about the mount. We also have the design load factors for the aircraft as well as crash and emergency design loads based upon aircraft certification requirements, factors of safety, etc. From there these external loads can be computed and used in the design requirement as external loads to a 'black box', that is an as of yet determined structural assembly for the pylon.
The exact design of the pylon and associated mounts are going to depend on these figures. Pylon design uses similar structures from OEM to OEM and its based on their years of experience designing these thing based on both expected mathematical models as well as flight test data. Unfortunatly the exact details of how and why it's designed the way it is remain a proprietary trade secret of the OEMs and they are not likely to talk about it. Boeing, like KFC, has a secret recipe for its wings and is not freely released to the public. The same is true for its pylons, empennage, etc.
The basics are most new pylons will be based upon this proprietary structural arrangement used in previous designs. The design loads and basic configuration of the parts an assemblies going into the pylon will have been calculated by a stress engineering group into sizing for the geometry of the parts to be designed. The first pass at the assembly design will be done by the pylon group, then used as a basis by stress for sizing and this iterative process will be repeated until an acceptable design solution is found.
Ground and flight tests will be the ultimate proof of the design and also usually leads to a weight reduction process to reduce part geometry of excess material once the actual flight loads have been verified.
Your question is an interesting one and it may be more beneficial to consult with either a retired employee from an aircraft design company who worked on these structures or a scholar in aircraft design. Your school could probably forward you on to someone like that and you can consult with them about this.
After doing so, it might be beneficial to take a trip out to an aircraft boneyard and examine an existing engine pylon on an airplane like a 737, 747, DC-10, etc. Heck, if the airplane is decrepit enough or about to be sold for scrap, ask the manager how much it would cost to amputate an engine pylon (minus the engine!) and take it back with you for the Master's project. You could examine it and build CAD and FEA models of the unit, then test these using expected loads for the aircraft and engine in question. While this might not answer your immediate questions, it will provide your project with a treasure trove of information about how and why an engine pylon is designed the way it is. You can then examine other OEM pylon design and dissect and analyze them very accurately based on this previous experience.
Hope that helps!