Gilee, there are several side effects to the stock ecu not getting a tach signal (which I covered how to deal with each one), so you may wish to try leaving it connected to the stock ecu like corbin's setup, and trying his method.

I can confirm the spikes I was getting was not caused by the alternator, not the stock wiring, as I drove around with the alternator field generator off and the sensor wired just to the MS, and was still getting the spikes with the default 420a MSnS setup.

Using just the opto circuit on the v3 board is the problem. It may be the 5v power to the opto circuit isn't stable enough, or the tiny capacitor in the circuit which makes the optoisolator WAAAY to sensitive.

The VR circuit is the way to go, but you must run it like I did if you don't want the stock ecu hooked up at all.