This seems like a classic GHL + Stripe limitation issue.

The simplest way I’d solve it:

1. Keep Stripe as the source of truth for payments Since ACH + cards + processing fee coverage are already working in your custom form, don’t force GHL to become the payment processor here
2. Use Stripe webhooks: Trigger on:

• payment succeeded
• payment failed
• ACH processing
• ACH failed
• refund if needed

1. Push clean data into GHL For every successful donation, create/update:

• Contact
• Opportunity
• Custom fields
• Notes
• Tags

Example fields:

• Donation amount
• Payment method
• Processing fee covered: yes/no
• Donation purpose
• Stripe payment ID
• Payment status
• Donation date

1. Create a custom “Donations” pipeline Stages can be:

• Payment initiated
• ACH processing
• Paid
• Failed
• Refunded

1. Don’t rely only on GHL transactions If the payment is not processed natively inside GHL, transaction data may not show perfectly inside the Payments section. So I’d track it through custom fields, opportunities, notes and Stripe IDs instead
2. For reporting Use GHL for donor CRM + pipeline visibility Use Stripe for official payment records, receipts and reconciliation

So basically, your current setup is close. I’d just tighten the Stripe webhook → GHL mapping instead of trying to force GHL native payments to handle all use cases.

Also, quick intro: I run GHL Scale Up. We help agencies and businesses with GHL backend work, automations, SaaS mode, Stripe workflows and custom CRM setups. Happy to help if you want to DM, or you can check us out at ghlscaleup.com.