What is the actual response time of your thermocouple in this system?  The 1102 has a fixed lowpass filter at 2Hz.  For most thermocouples this is fast enough and is why it is recommended over the 1102B/C in the catalog, however if you system actually has a higher bandwidth, then you could be losing useful information.  If your thermocouples respond significantly faster than 2Hz, I would recommend the 1102B, which has a cutoff of 200Hz.  You will need to sample faster to prevent aliasing (maybe 1kHz per channel), but this should not be a problem with the 6035E.  You can then filter the data in software down to whatever bandwidth is appropriate for your system.
Regards,
Brent R.
Applications Engineer
National Instruments