Communication timeout - reset send buffer block

Firstly, I ordered this kit and built it.
[www.amazon.com]

I had it and running and printed a few test prints, after which I took some time to calibrate things and had to file down part of the acrylic frame because a screw was catching on it whenever the bed moved. When I turned my printer back on it shorted out and burnt a hole in the ramps board. (I think some filings got in the power supply because of a careless mistake I now regret) I quickly unplugged it and order a new arduino and ramps board. Here are the links for the specific replacements I ordered:
Arduino: [www.amazon.com]
Ramps:
[www.amazon.com]

After replacing the parts I reset the voltage on the stepper motor drivers to .55 and uploaded the code found here:
goo.gl/csU6RI

When I connect it with repetier host I get this:
13:49:56.736 : OpenGL version:4.3.0 - Build 10.18.15.4279
13:49:56.738 : OpenGL extensions:GL_EXT_blend_minmax
13:49:56.738 : OpenGL renderer:Intel(R) HD Graphics 4400
13:49:56.738 : Using fast VBOs for rendering is possible
13:50:02.777 : No start signal detected - forcing start
13:50:02.835 : N1 M110*34
13:50:02.835 : N2 M115*36
13:50:02.835 : N4 M114*35
13:50:02.835 : N5 M111 S6*98
13:50:42.922 : Communication timeout - reset send buffer block
13:50:42.925 : N6 T0*60
13:50:42.926 : N7 M80*28
13:51:28.855 : Communication timeout - reset send buffer block
13:52:17.854 : Communication timeout - reset send buffer block
13:53:06.856 : Communication timeout - reset send buffer block

Note: any manual commands sent don't go through (commands waiting), but that's expected with the communication timeout.

The port is set correctly and is not on auto, the baudrate is set to 250000 on both repetier and marlin. I tried to change the baudrate on both to 115200 but when I tried to upload the code to the arduino I received this error:

avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
An error occurred while uploading the sketch

The board is set as: Arduino/Genuino Mega or Mega 2560
processor: ATmega2560 (Mega 2560) the port is selected correctly.
I have no idea what is causing this error. I've tried uninstalling and reinstalling the latest version of arduino. Updating USB drivers. Replacing the board. Etc. But I can only get the code to upload the very first time (right out of the box, first upload for the board) and any time after that I get that error.

I have wasted countless days trying to troubleshoot this but I keep ending up with this communication error. Any help is appreciated, I've read several forums and nothing has fixed this.

In marlin config.h make sure you set this as 0

#define SERIAL_PORT 0


Is the printer port visible in windows device manager ?

Hi all,
I have got a similar problem I have recently built from scratch an i3 clone with auto levelling and a home made mixing nozzle based on the diamond nozzle, I have upgraded the electronics from sanguinololu on my last printer to arduino mega 256 and ramps 1.4 with an add on stepper driver running from the aux pins to run the third extruder and a smart controller screen. I have uploaded Marlin firmware and overcome nozzle blocking and auto levelling I can move all axis manually run the homing routine and the bed levelling routine, control the temperature etc but I cannot figure out why gcode causes problems, when I load a gcode routine which has worked on the old printer or a newly sliced routine including G28 and G29 commands they will not run, they start as normal with the G28 and go on to complete the G29 levelling routine ending with homing all axis and then raising the temp to the desired levels and then for no apparent reason the nozzle moves to the print start position, stops dead and then the arduino re sets it self and the code is lost and the temperature plumits, this happens both with printing from SD card and from pronterface, I read somewhere that in pronterface it could be the baudrate being too high but I have tried lowering it by two steps from the 250000 to 115200 and 57600 but that does not alter the results I have tried various feed rates, altered the jerk settings, both up and down from the default settings. Can someone please suggest what might be the reason or suggest any trace commands for the errors that happen,