Just chiming in with my experience here. I too needed to use a custom certificate with Anyconnect, instead of the Meraki provided cert. I bought a Comodo PositiveSSL certificate from SSL2Buy. When the certificate was issued, I received a zip containing 4 files.
<mydomain.com>.crt << this is my certificate
AAACertificateServices.crt
SectigoRSADomainValidationSecureServerCA.crt
USERTrustRSAAAACA.crt
The latter 3 are root CA or intermediate CA certs. When configuring the custom cert in the Meraki dashboard, you are prompted to upload (1) your certificate and (2) the CA chained bundle. My cert if obvious, but I didn't know which of the others are the bungle, so I tried each of these 3 and it failed.
After chatting with SSL2Buy's support, they suggested I would need to create this bundle myself by copying/pasting the 3 other certificates into a new crt file in this specific order, one directly on top of the other.
1. USERTrustRSAAAACA.crt
2. SectigoRSADomainValidationSecureServerCA.crt
3. AAACertificateServices.crt
This bundle crt was then uploaded and accepted by the dashboard. I hope this helps others in a similar situation.