My transmitter works via pulsing. What this means is currently it might take 1-2 minutes to fill in my Agilent with data and then I visually do a reading. Does your device have a max hold API command AND can I then issue a command to capture the data file after a period of time?

Yes, the device does have a MaxHold mode, which can be enabled by setting the SPECPROC variable (0x0C) to 1, the max power value can then be read from variable MAXPEAKPOW (0x90).