Hi the trigger re-arm time of the 2204 is approximately 70 milliseconds on average (depending on PC and overheads).
Looking at your application the 2204 will not be be sufficient what you really need is a device that has larger memory and has a rapid block mode capture.
To explain further you will need to capture your data in block mode, normally the trigger re-arm time is too slow as it has to transfer each capture to the PC , however with a device that has rapid block mode the trigger re-arm time reduces to 1 or 2us depending on the device you choose. It does this by storing all the captures on the memory and then transferring it to the PC when the specified number of captures has finished ( as opposed to transferring each capture to the PC). For this to work in your application you will need a device that cans store more than 500k Samples, as you want 5k samples per waveform and you have 100 captures.
This brings you into the 3000 range, the 3204A has 4MS of memory and the 3204B has 8MS, any of these will be more than sufficient for your application. Just to let you know the difference between the A and B, apart from the memory the B model has an Arbitrary Waveform Generator which allows you to create your own waveforms rather than use a set of standard signals.http://www.picotech.com/picoscope2000.html
Hope this helps