I'm just trying to get something clear in my mind...
When you say the sampling rate is 100 sps time 3 channels, do you mean the PC is receiving 100 sps per serial port at all times, or do the instruments acquire data at 100 sps and transmit the data at regular intervals and you read all data available on each of the instruments.
The difference is that whether the PC is doing the acquisition work or if it is the instruments. It may have an impact on the proposed architecture. If the PC does most of the work, I might suggest using daemons to aquire at 100 sps on each channel. If it is the intruments, then the acquisition may be done as part of a state machine which is located inside the same loop as where I would place an Event Structure.
RayR