OK, so it looks like we're talking about a facility claim, so we're talking about the facility level, not E&M levels here. So facility levels are not based on documentation but rather on the costs and usage of facility resources - as far as I know, it is not an industry standard or coding requirement that facilities or payers must follow ACEP on this. Typically, every facility will develop their own internal guidelines as to how to arrive at these levels, but if your facility is using ACEP and the payer is using a different set of guidelines, then of course there are going to be differences, but you're taking the right approach by auditing based on the payer's own guidelines. It won't help you to argue a level is supported based on ACEP guidelines if the payer contract says that the level and payment will be determined by the payer's own policy.
Without reading those guidelines and the specific language, it's hard to guide you on this, but basically you'll want to identify cases where the payer is not following their own rules. If their policy is written in such a way as to state that the level will be determined by what other services are billed on the claim, then it won't help much to look at documentation or nurse's notes. But if the policy says that levels can be determined based on the content of the medical record and the documentation as to what actually took place during the encounter, and they are just making assumptions based on what they are seeing on the claim, then you have a better case. If so, I think what I would do in your situation is to find some good examples where the level they paid is clearly contrary to their own policy, and present these to your payer.
But you may want to look carefully at the language of the contract. Some contracts could be written in such a way as to allow the payers to make you 'guilty until proven innocent' - in other words, the payer is allowed to just look at your claim and make a judgment that your level is wrong, and then it is up to you to prove otherwise and you will be stuck just appealing these on a case by case basis.
Ultimately you want to show them that the claims pricing practices are conflicting with their own policy, are in violation of your contract, are costing your provider money in underpayments, and creating an administrative burden to correct. Payers these days fortunately are becoming a little more sensitive to the impacts their policies are having on providers, especially facilities, and they should be willing to work with you on this.