Mal,
I have modified your VI to allow you to set the buffer size, as well as separating your output into two separate waveforms. For your first problem (the -200279 error), I have added the DAQmx Configure Input Buffer.vi. This will allow you to set the size of the buffer you are reading into. It is important to remember, that if you are getting this error, it is because you are not reading data out of the buffer fast enough. This could be caused by doing CPU intensive operations (i.e. .. FFT, auto-scaling charts/graphs, etc)on a slow computer, or having a lot of other things running in the background. If this is the case, increasing your buffer size will allow the program to run for longer before it errors, however it will not really fix the problem. However I was able to run your example at a sample rate of 100 kHz on my 1 GHz computer without error.
As for the data, using the 1D Wfm-NChan NSamp read flavor, you will get a 1 D array of waveforms back. This array will contain a waveform for every channel in your acquisition. The order of the array will match the order in which you specified your channels. To separate these channels, simply use the index array function to index into the array to the channel you are looking for. I have also added this to your example VI. Please let me know if you have any other questions.
Hope this helps,
Dan