Wire length, EMI and comms failures
So, I would like to do an analysis on the wire lengths in my system
  and its impact. How can I do that ?


If you know the current on the line and resistance, then you will know how much voltage it will generate when the return current goes through the ground. This can be modeled on paper. Either measure the wire or find an AWG chart and estimate it. This type of noise from switching return currents is called common mode noise. 

Another thing you will need to account for is inductance, each wire functions like an inductor because when currents flow through a conductor they generate a magnetic field. There can be mutual inductance from one wire to the next when wires are ran together, it may be necessary to design the cable with a transmission line for the return current of the signal. Or use twisted pairs to reduce this effect.

If you can estimate or measure the inductance and resistance, you can use a spice package such as LT spice to model parasitic effects. At speeds over ~50MHz transmission line effects and capacitance will also come into play, however these are harder to model and are probably best measured. 

In any case, you need to be able to take a cable and reduce it into a circuit. Remember that a wire has resistance and inductance, if you have two conductors and an electric field between them, you have a capacitor. The real world its too difficult to model all that goes on, you will never have a perfect model. The goal is to try and model all of the relevant dynamics in a circuit so you can get the answers you need to come up with a proper design.

There are also 3d FEM field solvers that you can draw parts up with 3d cad programs and tell the solver what kind of current or voltage is on the wires, the solver then solves all of the EM field equations and can give you the answers. In almost all cases, this type of analysis is just as time consuming as testing the actual physical wires. With the cost of such software in the 10k$ it's usually not worth it. 


  Are there any tools that can help me automate the whole system ?


No, you will need to do this yourself. 


  Also are there any simulation tools or papers that can help me proceed
  in this ?


A good start would be to read Electromagnetic Compatibility Engineering by Henry W Ott