Your strategy should work just fine. Did you check out this webpage Auxiliary Trigger?
You will have to purchase another type of NI breakout box if you want to record time stamps to the Tiff file as you can see from the above page.
You will have to write a custom script that does something like: detects your "stimulate now trigger", shuts imaging laser shutter, closes the shutter to the PMT, turns on the blue laser, turns off the bule laser, and reopens the closed shutters.
If the PMT shutter is configured in the ScanImage MDF, all you need to do is something like this (Matlab):
% deliver stimulus
These commands shut (false) and open (true) the shutters.