[HooperPC]

Bought this 2006 E83 from a so-called dealer as-is with 'electrical problems', no start, dead battery. I knew this could be challenging, but it is a clean history, no accident car, no dents, solid interior, advertised with low miles. And I already own an '06 X3. So I figured, its was a risk worth taking and had some extra time .... well at least I did.
Replaced battery, ground straps, starter, plugs, CCV, and fixed wiring problems in the dash. The car will start, but only after several seconds cranking sometimes need gas pedal. Fuel pressure and pump are fine, no intake air leaks, and engine harness wiring is good.
After pulling codes, replaced the crank position sensor. Twice. Second time from FreeCP.

I keep getting these codes. I can clear them, but next time I crank it, they return.
299A - DME: CAN fault management EGS
3C1D - DME: Crankshaft sensor: signal
5F21 - DSC: Engine management: interface
5EB1 - DSC: Steering-angle sensor, supply
5F42 - DSC: Transmission control, limp-home operation
0096 - EGS: CAN engine speed
0091 - EGS: CAN torque reduction
The CKPS code always set first, and the other codes cascade from it.
Anyone seen this before? I have been stuck at this point for over a month! HELP

[unixnerd]

Some of those sound like low voltage issues. Are you getting 14.4V when it finally starts? I'd check the engine ground too. There should be 0V between the engine block and the body ground. My Z4 had a 2V difference because a nut on the back of the starter motor was only hand tight.

These can be very picky about OEM position sensors.

[HooperPC]

Thanks for your interest. I was able to get a bunch of help from Bimmerfest and E46 fanatics on this M54B30 X3. The MS45.1 DME was the pivotal problem. I did replace the Intake and Exhaust Cam sensors with new OEM, but this was not necessary.
After much diagnosis (several hours), reading voltages with sensors on and also removed from the car, checking harness connections, confirmed that the DME was not reading the Crank Position sensor voltage properly. It read 0.2 V at all times. I then engaged an expert who demonstrated how to use WinKFP to flash software updates to the DME. After that 5 minute process, the car started right up! That problem has not returned.

However, the X3 still has intermittent electrical issues with the ZKE (general module) where it loses sync with key remotes. Also, the EWS will occasionally lose sync with the DME, set Code 2737, and prevent the car from starting.
Still working on those annoying issues.

[unixnerd]

Things like that can often be a bad ground. There are loads of ground points all over the car. It's worth disconnecting the battery then undoing and cleaning all the grounds. One classic sign of a bad ground is to turn on the side blinkers and see if any of the gauge needles "tick" slightly in time with the blinkers.

Water damage or rodent issues can also cause this. A friend bought an E32 we knew had mice problems, I told him not to. Sure enough the car was never right.