The Motorola 16 pin Accessory Connections and Functions

Pin Description and Notations 
1 External speaker negative out - Both hot and negative sides of the speaker amp are floating and should never be tied to ground. 
2 Transmit Mic Audio Input  80mV RMS @ 3KHz Deviation. The audio here is pre-empahsized to the TX Exciter. (This is paralleled with mic jack, so if you use the mic in addition to the rear accessory some audio loading may occur - adjust your Aumix settings accordingly)  You might also want to insert a 10uf Cap in series with this line to block the DC voltage (powers stuff in the mic) that may effect the op-amp performance in your soundcard.
3 Transmit PTT (grounding this pin, transmits the radio)
4 Programmable - but normally an External Alarm Output 0.25A max. In some radios it can be programmed to COS output
5 Flat Transmit Audio 150mV RMS @ 3KHz Deviation  This audio is not pre-emphasized to the transmitter, commonly used to send external CTCSS or DCS audio signaling or as a flat input from a receiver that delivers un-processed audio.  If you use this input for your IRLP audio out without proper processing, it will lack crisp fidelity and can over deviate the transmitter.
6 Programmable. Can be programmed as a TX PL Inhibit - if you wish to use the an AUX line from the IRLP Board to trigger this port while sending your link radio CWID, with some of the clever ID scripts available.  CWID can be sent from the IRLP link without PL - to keep it off of your repeater if its receiver is using PL decode.
7 Ground - Although this is Signal ground, I would suggest that you run an additional low resistance ground between your Radio, Power Supply, Antenna Ground and Computer Ground to avoid audio ground loop hum. 
8 Receiver Carrier Open Squelch - COS going Low,  but can be programmable for COS high and a few other functions in some radios.  If PL decode tones are programmed in, this logic is "ANDed"... that is - both a COS and PL decode signal must be present for the logic to go low at this pin. Remember to "hang-up" your mic to externally enable PL decode, alternately by making an RJ45 mic jumper with pins 3 (PL) and 4 (ground) to turn on Receive PL.
9 Emergency Alert Input (you will commonly see this pin tied to ground on the stock 16 Pin jumper plug that forces the alarm inactive, no matter how it is programmed)

Stock Jumper 
9 and 7 Alarm Disable
15 and 16 Internal Speaker
0 Ignition Control Input. If programmed active the radio will not power up until this pin sees +12 volts. We recommend that it be programmed inactive unless you have need to "wake-up" the radio from an idle state for some reason.
11 Receiver Discriminator Audio Output. On most radios there is a jumper on the Logic Board that affects the audio state of this pin. The internal jumper is selectable as Flat Audio or De-emph audio.  You want the De-emph position for IRLP and for reference, its about 350mV RMS @ 3KHz Deviation
12 Programmable
13 Switched A+ Sense 0.5A max.  Caution what you hook to this input, shorting it or loading it down could possibly blow an internal fuse that will render your radio powerless.
14 Programmable
15 Internal Speaker + This is the high or hot side of the internal speaker.
16 External Speaker + This is the audio amplifier output that can jumper to the internal or external speaker for local use.
Tie 15 and 16 together to enable the internal speaker or use 16 + and 1 - for an external speaker. Again, these are floating and should never see ground without a balancing transformer, so they should not be normally used to feed an external line level source unless conditioned. Besides, you may want to monitor the local radio traffic coming into the node by turning up the speaker volume -  without affecting the audio level going to the soundcard.