Since the shield does all of the decoding, all the Arduino does is send commands over serial. Which you could do with software serial.  That leaves tons of resources for you to do other stuff.

Going into my next performance review: 

"You have lot of voltage, you just need to apply yourself to your wattage."

How often do you find yourself using the word "Amperage"?

Depends in what you mean by "power"

It really feels like this post is missing something...

Using the same color wire that overlaps makes it almost impossible to see what is connected where.   Also, you are missing the Arduino connections.

Reverse engineer your own circuit.  Draw a schematic based on what you have wired up now (without looking at the reference).  That will help show thr differences.

The MSEQ is expecting line level voltages.  That miceophone's per-amp may be over driving the input.  Put a 470ohm resistor in series from the mic to the MSE's input to see if it changes anything. 

[and does not recognize the device connected to that port]

I'm working with the Arduino ethernet, I'm using the library but I have problems with the serial port before and does not recognize the device connected to that port.

What doesn't recognize the device?  What device?

If you can provide me with the correct one I'll be thankful.

The links already were?  In the post you quoted and the one before it.

Why does it show a red ON and the LED blinks red.

Official boards do not have red LEDs.  (Or any ability to "show red.")  Cheap counterfeit boards are, well, so cheap they use red LEDs since they are the cheapest. ($0.0001 vs $0.000125 king of savings)

PLease help.

Contact the person / company you bought the board from.  Perhaps by using cheaper quality components and manufacturing processes they are able to provide personalized technical support instead.

It was working fine for Arduino Due board that i was using previously.

Due or Duemilanove?  They are completely different.

atan2() takes radians what are you giving it?

Keep in mind services like Ponoko offer this already.

My experience with 3D printing has been that it really needs to be iterative to be effective, which means, sending files to someone else takes too much time.

Everything Is working fine I added a MEMORY checker to the sketch and there is 800+ bytes ram free.

Since the microcontroller used doesn't have a memory controller, these sketches are estimates at best.

I reduced the occurrence of the problem by adding the following code..

Post the rest of the code.

Why do you keep calling Serial.end() followed immediately by Serial.begin()?  That seems completely pointless and creates the very real possibility data is coming in that you are going to miss, resulting in junk eventually.

I am pretty sure its a firmware/arduino problem as :

It's almost definitely a code problem, so post all of your code.  There is no "firmware" running on the Arduino after the bootloader jumps to the code vector.

2)The PI is powered from the same Stepdown Voltage regulator as the Arduino, and it does not crash so I think this eliminates the PSU.

The Pi is a completely different system, so I fail to see the connection.  Also you haven't verified the Arduino is "crashing."  Again, it is probably problem with your code not the hardware.

3) The program continues to run even after the serial port has crashed

The serial port cannot "crash."

I am also going to add a couple of 1000uF caps To the 5V rail to eliminate Power outs.

That's great for low frequency ripple.  1.0uF and 0.1uF will help with high frequency.

Is there a known issue with running the Hardware serial port Continuously @ 57600 ?

No, not at all.  Plenty of people do this without any issue.

Yes, return to shop.  Why waste more time troubleshooting?  It arrived broken.

 I guess you differentiated between physical size and value in your original post, I just didn't quite understand why you would be asking.

One point to make, the smaller a ceramic capacitor (except C0G/NP0) is, the higher its voltage coefficient.  So if you put 5V on a 6.3V 0402 and a 1210, you're going to get more capacitance from the 1210.

What do you mean by size?  Physical or value?