So, the original post asked for suggestions and there are a lot of good ones in this thread already.
If I might offer a few thoughts?...
 
1.  Get the source files from your client in platform native files (.avi and .wav for PC and .mov and .aif(f) for MAC).  This can be difficult for every client.  Sometimes, we can work with what they have and sometimes we have to convert their files (which should be added to the invoice).
2.  Have them select no compression, raw, or a lossless CODEC.  This can be difficult when working with FCP houses as they may not have ever looked into these options or understand them.  Again, we may need to convert their files.
3.  Verify the technical specifications of the file with your client.  Make sure you know exactly how many frames, how many samples, sample rate, bit depth, channels, exact TRT... anything that you can spec to make sure your file is in sync and will work for your client.
 
We all do lots of different Sonar projects for many different reasons and pay scales.  If a client needs sample accuracy and is only providing compressed .mp4 files, we need to examine that project for budget, time, future work, client development, ect... the list goes on.
 
If someone wants to know my workflow, I am happy to offer it.
 

dlion16
really, as much as i love sonar, it is a daw, not a video editor.
 
i use vegas for sync-type things. if i'm doing dialogue unless there are issues i can probably do all i need in vegas, i have many of the same plugins available. i'll bring a problem clip into sound forge if its really bad. 
 
i use sonar to work on individual music tracks (bedding) and when i need 1:22 of a song with vocals, i'll export 1:45 and make my cuts and sync in vegas.

This is what I do also. This is because I have had similar issues that the op has. I only use Sonar to edit audio, then I export only the Audio. I bring that into Vegas and line everything up. The problem with avi files is that they are huge compared to mp4 files. If you deal with high definition video then this can be a problem. 
 
Typically I will export a mp4 file from Vegas bring it into sonar and work on the audio. Then I will export the audio and bring it back into Vegas for the final render.

Anderton
I'm confident Microsoft will nail down the loose ends on their Media Foundation platform eventually.

Not to sound belligerent or anything, but I've been waiting for Microsoft to 'turn pro' since I came over from the Amiga platform in 1994. After 22 years, I'm still waiting for them to adopt the leading edge for things like video and audio production.
 
Their main focus is and always has been business. Their built-in support for video and audio has always been aimed at what a business will find acceptable to fulfill their everyday needs (in-house presentations and marketing support).
 
Just saying.

Noel Borthwick [Cakewalk]
Hello, we'll take a look at this. I haven't noticed any sync issues with MP4 when I tested.
Can you provide a sample MP4 file and simple project that exhibits the problem? Put it on a file share and send me a link...

Hi Noel, you were going to look into the issue of Sonar not exporting audio in proper sync when session contains a video file such as an MP4 or quicktime file. It's been a few months, just wondering if you found anything with the files I sent you for testing? This is a pretty major issue for film/tv composers so I thought you might put it on the front burner. Could you let me know? Thanks
Jono Grant