Multi-channel high frequency signal acquisition
If you use a Superheterodyne Receiver type design, you can mix &amp; remove all or most of the 100MHz carrier signal in one or more het. stages (maybe a 70MHz stage for 30MHz IF, then a 29MHz stage to 'final' 1MHz IF). 

This way, ou can use less costly filters &amp; circuits to "narrow in on" your envelope of interest.

Then you can add a tuner to select between your predefined channels, to test a single channel at a time (using only one DAQ for all channels); or you can skip the tuner, and use a series of filters to split out all of your 1000+ signals for 'simultaneous' testing (at a few hundred times the price, due to needing 1000+ DAQs).