BMW Repair: SMG issue, e46 m3, independent shop

Question
Evan, hope you can help.  I have a 2002 E46 M3 with approx. 40K miles on it, the vin is JR14399.  The car has been flawless since my purchase.  A week ago I parked the car as normal ran inside my house and five minutes later jumped back in the car, put my foot on the brake and pulled the car into neutral to start, the indicator showed "0" in the dash.  When I hit the key the car did not start, all of the electronics came on but the car did not even turn over. The SMG light on my dash board lit up, and when I put the car in reverse or over into the drive position it would blink. The brake pedal felt hard and did not depress like it normally does, this is not the first time the brake pedal felt like this, sometimes it feels stiff and then when the car starts it depresses to its normal bottom point.  The next morning I jumped in the car did the same routine and the car started and ran fine! Three days later, got into the car and the same thing, no start except this time the shifter is in neutral position and I can not move it into either reverse or drive.  Took the car to a local independent shop I know and trust and they said although the scan shows a code for the trans it does not give any specific info as to what is wrong, they suggest I take it to the dealer which I do and they say that they think they can fix it if they replace the ECU control unit and Hydro unit which will run me about $6000.00.  
the car showed no sign that anything was wrong the first time it did it, and then drove fine for 3 days, I am having a hard time believing that the entire SMG portion of the trans could die at once, both the electrical and hydraulic systems failing at the same time seems impossible especially since it came back to life for 3 days and then died again, and I am fearful the dealer has no idea themselves and that they are just replacing everything to fix the issue.  My independent shop did show me a BMW technical service bulletin SI B 23 03 06 that says any dealer working on an SMG issue should contact Getrag through the PuMA system for a specialist, but I do not believe that this happened through my dealer.
Any insight, or suggestions would be greatly appreciated, I am in Southern CA if you happen to know or suggest someone local that can help me.
Thank you in advance for your time.

Answer
Justin, try replacing the hood contact switch. If the hood is open the car won't shift into gear but should start if the car is reading neutral correctly. Try opening your hood and starting the car and try shifting the car. Does it do the same thing as when your car doesn't shift before?
SMG has had many issues with SMG relays and related wiring. See if your car has had the SMG relay and relay wiring pin changed if applicable to the service action.
I would change dealers since there are soooo many on SOcal. An independent shop would have no clue what to do on a system like this. If the relay, hood switch, relay wiring, or the SMG hydraulic pump,(most common failure items on this system) don't fix it be prepared to spend money on extensive diagnosis at a dealer. Insist that the shopforeman work on the vehicle so you know he has the training and experience on the system. They will need to be able to duplicate the problem while it is happening. The nicer you are to the service department the more likely they will be willing to help you in any aspect of your repair. Have them diagnose it. Is it an electrical issue? Hydraulic issue? Speaking of which check the SMG reservoir by the intake manifold.
-Evan