Debugging new hardware can be difficult and trying. The most common mistakes that most new engineers make when first debugging a system are: trying to debug too much at once, not testing their assumptions, and keeping inadequate records. Jumping the gun to complete functional testing of any new, highly complex system is, as you have discovered, a waste of time. A more experienced engineer would first break the system into pieces for the initial tests, because he would recognize that there are likely to be a multitude of problems.
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