Unable to connect MP to Megapirate via 3DR radios.

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What steps will reproduce the problem?
1.Setup 3DR radios and verify operation via AT/RT commands.
2.Start up Mission Planner and attempt to Connect.  MP times out with no 
heartbeat.
3. Connect to flight control board(Crius AIOP V1) via USB and successfully 
connect via MP. 

What is the expected output? What do you see instead?
Should be able to connect via 3DR radios with MP.

What version of the MegaPirateNG are you using? 2.8_R3.  MP version is 1.2.53.

Please provide any additional information below. I have searched through the 
code to see if I could find where the serial port switches from the usb port to 
comm3 and can't find it.  This probably doesn't mean anything because I 
probably didn't know what to look for or where to look.

Original issue reported on code.google.com by jbower6...@gmail.com on 6 Jun 2013 at 2:26

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Just thought I would add that I don't believe the software is shifting the com 
port from Com1(USB port) to Com3.

Original comment by jbower6...@gmail.com on 6 Jun 2013 at 7:28

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Just tested 2.9.1 and it behaves exactly the same.  Radio's are connected and I 
can query them from either the 3DRRadio software or from the terminal within 
Mission Planner.  

Original comment by jbower6...@gmail.com on 6 Jun 2013 at 10:07

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I was able to get the radios working by connecting the remote radio to the 
TX0/RX0 signal that is used by the usb port.  This does not mean that it is 
fixed because the correct method is to connect via the TX3/RX3 port.  I believe 
that the mavlink data is not being switched to the correct port.  

Original comment by jbower6...@gmail.com on 7 Jun 2013 at 10:52

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Serial3 port works by default with 57600 speed, Serial0 = 115200. So maybe you 
must just change port speed in 3DR module to 57600, or change Serial3 speed to 
115200 in APM_Config.h

Original comment by Alexey.K...@gmail.com on 14 Jun 2013 at 5:55

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Sorry, you can change the Com 3 baud rate to whatever you want and it 
still will not connect to Mission Planner.  The radios will connect to 
each other but no heartbeat with Mission Planner.  The only way I got it 
to connect with Mission Planner was to use Com1.
Perhaps it is time to modify system.ino to eliminate the looking for the 
USB_MUX_PIN and automatically configure Com3 port.  I don't know why you 
need to look at the USB_MUX_PIN since it doesn't work and you have to 
switch Com ports in Mission Planner from using the usb port on the fc 
board to using the com3 port.

Original comment by jbower6...@gmail.com on 14 Jun 2013 at 2:15

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[deleted comment]

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I am using the last approved version which is 2.8_R3.  have not tried the 
2.9_R3 because I heard there are problems with it. According to the code, the 
when there is no USB attached the code is supposed to shift the input from the 
usb port to com1 and it does not do that. Have you had any problems with 
2.9_R3? I tried using com3 and could not get heartbeats with it.  

Original comment by jbower6...@gmail.com on 18 Jul 2013 at 12:09