I will try to help, based on what I know about prolonged service codes, and for how to charge for your services. (Hopefully others will jump in with their advice also)
The 99215 is for an average of 40 minutes FTF between provider and patient. You have a provider who spent 360 minutes with a patient. So taking into account the 40 minutes for the 99215, that leaves 320 minutes of prolonged services that need billing. The 99354 accounts for the first 60 minutes of that time. So now you have 260 minutes left to bill. By billing the 99355 at 9 units, you cover the remaining time, and it is legitimate, since you only need 15 minutes of the 30 minutes for a 99355 to bill it. Everything I have read says that the 99355 as an add-on code has NO limit to units that can be billed.
The billing would then be:
99215(1 unit)
99354(1 unit)
99355(9 units)
All of that said, I can see where the claim may need the treatment note sent in, for Medicare to review. If the claim continues to deny, I would absolutely do that, assuming the documentation on time spent is very, very clearly spelled out. There are numerous articles on the internet about how prolonged services should be billed, that you can check out.
As for how to charge for the services the office would like you to perform, my opinion is that you need to do this for an hourly fee. What that hourly fee should be can only be determined by you, but it should be somewhat high, because auditors get paid quite a bit for their services, as do consultants, and that is basically what you would be. You could start out by reviewing their most billed codes, making sure their fees are set correctly, then move into auditing/reviewing a sampling of their claims. Then from there, set up a process to monitor their billing. At some point, you shouldn't need to do that anymore(or can do it maybe quarterly or something), if you have them properly educated on what they can and cannot bill, and you see that they are following your recommendations.