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.