I don't know what your planning, but i would definitely go with the megasquirt unless you are running the brain that came with the motor and you haven't made MAJOR changes to the motor. Problems with running the stock ecm vary depending on your situation. Need the proper software to tune it which is probably the hardest thing. I have a good friend who specializes in Ls and Lt tuning and has all the software so I bring in him for those scenarios. I am more than happy to answer any questions I can. I am still learning on this stuff but I'll try.