Had another at getting the MicroSquirt running on the GTS1000 today, and I used my long loom to piggyback off the existing ECU, but I was only connecting it to the crank & cam VR sensors. After cranking the day before I had no cranking RPMs at all, so I double checked the MicroSquirt against my drill powered rig, and it looked like the MicroSquirt was corrupted, because it didn't crank on this either. Reloading the .s19 file into it and loading the .msq into returned everything back to normal.
I have an oscilloscope, and although I got a good trace of the cam, I got a poor one of the crank, it was full of AC noise. At the time I couldn't understand it, but after cranking this morning, I was non the wiser. I could run the bike up on the OEM ECU, and get intermittent RPMs running at half engine speed, but they would start until nearer 230 revs, and idle was showing 436 or so.
The centre stand on the bike was missing, so it's on it's side stand, and when the engine missed a little, the RPMs came back

but then they disappeared. I logged it and couldn't understand. I tried refining the pulse tolerance and still no better, after a while pattern was emerging, so I propped the bike up vertically, and the RPMs were good for longer...the crank was sloping downhill, and the tolerances must be just enough to affect the VR sensor clearances.
So you'd think now I'd have a cranking RPM, no chance. On the rig it cuts in at 120 revs, and I reliably informed the starter does 350 rpm on a good battery. I bootloaded the TachRef code into the MicroSquirt, and started sampling. When the engine was running off the OEM ECU and RPMs seen in the dashboard, I got a cam and crank sensor processed pulse clearly seen on the plot.
When I was cranking, I only saw it once, and that was after swapping the VR sensor for another one with a stronger magnetic force, but still I cannot see any cranking RPMs. I reversed the polarity of the crank sensor and things were no better but the plot looked better.
I am still using Rising Cam Sync with Tach or Wheel in the Dual spark Options, but the half speed RPM figure is a mystery, it might even be a code error for this option, because I can't understand, why if I have two tach events per crank, it is wrong.

UPDATE
Searching the forums to find more about this and a post mentioned no of cylinders...

What a numpty, in between whatever, I now have 8 cylinders in the Injection Control box, whereas I did have 4 before
...this must be why I have half speed.
