What do I need to install for SONAR X3 Producer to be able to convert audio to MP4 (.m4a)? Will it then show up in the Export Audio choices?

It requires an external encoder. Here is a similar thread http://forum.cakewalk.com/FindPost/3225867
Rather than add the external encoder to SONAR, I would create a wave file with SONAR, verify the file is OK and convert the file outside of SONAR. That said, if you prefer to have SONAR automate the process of wave creation and calling the external encoder, the thread above details the process.

OP has a confusing question.An MP4 is a video file (with audio) and a m4a is an apple audio file....perhaps this can be clarified?

Yes, I'm looking for audio only conversion to m4a, preferably Apple Lossless format and not AAC, Is there a plug-in available for SONAR X3 Producer, or, if not, what stand alone program would do the job? Also, is there an mp3 plug-in that allows ID3v2 input? The one I have only allows ID3v1. Thanks.

iTunes (Mac or Win) will do the conversions but not from within SONAR.
 
https://support.apple.com/en-us/HT204310
 

Audacity will convert to M4A.
http://www.audacityteam.org/download/
This is free software.