Consider using signWithCertificate when building the JWT signature

Instead of passing in the private key as base64, you can sign by reference to a private key managed by the platform.

Check out this method:
https://developer.salesforce.com/docs/atlas.en-us.apexcode.meta/apexcode/apex_classes_restful_crypto.htm#apex_System_Crypto_signWithCertificate

Locate the Apex entry point that builds the JWT signature and read how it currently receives the private key. Review Salesforce's Crypto.signWithCertificate documentation, then verify that signing through a platform-managed certificate preserves the SDK's existing JWT behavior.

Written by the indexing model from the issue text.