First off, disconnect your injectors and your coil until you get a good tooth pattern while cranking.
The polarity of the signal to the power stage is selected by the confusingly named Spark Output "Going High" or "Going Low" setting. If you use the wrong one, it may overheat your coil and will trigger at the wrong time.
To check the crank VR sensor, you want to run a "Tooth Logger" view from Tuner Studio - see the MSextra Setting Up Guide for Megasquirt-2 (your MicroSquirt v2 is most similar to Megasquirt-2). If you get something, but still aren't getting rpm sync, post a picture.
You can also test the fuel pump, injectors, ignition and idle valve separately - see the Output Test menus under the TunerStudio CAN-bus/Testmodes tab, and the Setting Up Guide.
I looked at the schematics and I don't see any jumpers in the MicroSquirt v2. Unlike the MegaSquirt, you either wire up the Opto input or the VR input (not both) and the circuits will use whichever one is active (no jumper selection is involved). Does your MicroSquirt have some sort of plug-and-play adapter board, in addition to the main MicroSquirt board? If so, please post a picture showing any jumpers.