While it's not an officially supported feature, you can run more than one instance of StrokesPlus, to have different gestures for different mouse buttons.
For example, make a copy the StrokesPlus folder (since you want two different configurations, not to share the same StrokesPlus.xml file). I would suggest closing StrokesPlus first, then opening the copy in the new folder and setting the Stroke button and maybe even a different stroke color. Then start your main copy. StrokesPlus will prompt you to ensure you really want to start an additional instance, click Yes and you're good to go!
The only thing I've noticed is a problem is when you use the other instance's Stroke button as a modifier key in the current instance. The most recently started copy will work fine, but the first copy won't receive the other's stroke button event as a modifier since its hook is further down the hook chain. Basically, just don't set a modifier key to be the stroke button used by another S+ instance or you may have unexpected results.