Hi Parramatta,
Your approach looks like an elegant alternative method to using rail-rail instrumentation op-amps.
The MCP6S21 looks like a good choice with gain programmable from 1-32. In particular the MCP6S28 would give you 8 mux selectable inputs (via SPI) which you could read into one ADC port on the 40X. This would work out a lot cheapr (and simper - PCB wise) than using instrumentation op-amps [possibly slight loss of accuracy though?]. Also give you more effective analogue inputs.
Firstly let me say I haven't actually used one of these, but...
I believe that using the 40X you would use the dedicated spi pins, and then set up the SPI using hpisetup, followed by issuing the appropriate SPI commands using hspiout e.g. instruction register to set gain, and then channel. There is some sample SPI code - [you've probably already seen it] - on manual2 p68.
Then it would be a matter of reading the ADC pin on the 40X using the readadc10 command.
It goes without saying that careful PCB layout and cabling on the analogue inputs is important here in order to avoid extra errors in the readings.
Hopefully this has helped and good luck trying it out!
Michael