Rino,
Yes I can see why say it is not ideal. All of the newer AFEs like AFE5808A have the Samtec connector on the top instead of the bottom which makes it easier to mate with the TSW1250 and probably the FMC card.
I am not familiar with this Matlab code that you talk about, but I will look into it. Our new generation of capture card the TSW1400 has enough memory to capture all eight channels simultaneously.
Thanks,
chuck