Do conventional loggers on the stock ECU log actual injector pulse width? I am going the boomslang path for wireing, and I wanted to get good "stock" data logs befor doing any major mods.... but I didn't realize that stage 3 jacks with the fuel system without any map changes

Main reason I went boomslang is I will need direct control of the injectors with the setup I am running. On the E-85 I could probably tune by A/F maps, but if I need a gasoline map the injectors would be too big for the A/F maps alone to handle.
Looks like I will have to get my "stock" data logs with a conventional OBDII data logger after all. I am now very glad I am in on the group buy for the OBDII loggers.
Any other "gotcha's" I need to look out for with the boomslang harness? I know that if I am too agressive on the direct control of the injectors I can run into a situation calling for 100% duty cycle and in that situation the EMU gives 100% duty cycle regardless of what the map is calling for correct?
Thanks,
Keith