Why should an engine need to be partially or fully disassembled to determine a misfire. Someone is way, way misguided if they have to resort to this.
The most obvious would be spark plugs, coils, or worst case; low compression due to a tight valve. The compression issue is easily determined without disassembling any of the engine.
The warranty company sounds like a 3rd part outfit and stonewalling any claims are not rare although the TV commercials make it sound like they pay everything presented to them without question. Not.