2008 Nightster blackout 2-1 exhaust, air cleaner, Fuelpak ,relocated coil and wire tuck.

Ok so I was having issues with my negative cable from the battery last summer and after I was forced to ride in the rain started experiencing serious issues. The last time I rode, the bike sputtered after about 15-20 minutes and completely turned off. Check engine lights immediately lit up. I wiggled the negative wire a little bit and eventually made it home on one cylinder. Fast forward several months and I'm finally able to put some time into trying to diagnose the issues and get her back in tip top shape.

DTC's -p0132, p0152, p1354, p01355, b1121, b1122, u1016, b1006.

For starters, I ordered and installed new plugs, wires and battery. I fixed my negative wire and did a quick check on a majority of the connections. The fuse for the ECM was blown so I replaced it.

I then cleared my DTC's and attempted to run it, with the same result- back cylinder not firing. This time the only DTC was p1355 (rear ignition coil). At this point I thought it might be the ECM or Ignition Coil. I unplugged my Fuelpak also, still nothing.

When I pulled the wires from the plugs to check for spark, I discovered the rear ignition coil was not sparking. I then used the front coil that was firing the front cylinder successfully to attempt to spark the rear cylinder. This produced a spark but the rear cylinder still would not turn over.

So it appears only the rear coil of the ignition coil isn't firing AND when the rear cylinder receives spark, it doesn't fire (fuel line, pump???)

I'm kind of stumped at this point. Fuses, relays, pinched or corroded wires, ignition coil, ECM, fuel line, fuel pump? Any suggestions or advice would be a huge help because I am really quite inexperienced and just learning as I go.

I've read thru so many of the threads here and learned a lot but nothing seems to match up with this and I'm trying to avoid the dealership at all costs.

 

Here are three scenarios that come to mind:

The ignition firing sequence is controlled by the ECM, based on the signal from the CKP (CranK Position sensor), and this depends on the computer determining the compression stroke of each cylinder. If one cylinder does not have compression then it will not fire, if all other systems are go <-- from this scenario it may be worthwhile to check your cylinder compression.

Edit: may also be a bad CKP which IS a known issue with Sportsters in particular

I'm thinking a little rain did not cause your issues - that's unusual for most modern bikes BUT early EFI Sportsters were known to suffer corrosion in the fuse panel <-- might be a good idea to rip that apart and inspect closely.

If your regulator is kaput then you may be running AC current through your electronics, which can cause all manner of havoc, especially on an EFI bike. easy test would be to disconnect stator plug from regulator and run the bike on battery alone. If all is magically well then you'll be looking for a new regulator.