I think I got your patched open cart extension "working"
I did a test transaction, and send the coins - although I have not seen the coins show up in my bit-pay account yet. hopefully I am not out these coins.
Contact steve or support, the IPN isn't working and posting back. So the transactions will go through and get to bitpay, but bitpay isn't posting back to the sites to let your system know that there has been a payment. Something to do with the cloudflare proxy. So steve is having to manually send payment notifications via email to each client till it's fixed.
On the manual system, send me a PM with requirements. When the kitty litter hit the fan we made our own Bitcoin payment module for WHMCS that interacts with bitcoind without a third party. It's quite simple really just need a DB to keep track of invoices and transaction's. So it's already made by us to work with bitcoind, we would just need to change it to opencart.
Plus if you don't already have a bitcoind instance running we have bitcoind cloud hosting to offer. So PM me, it's already out there and made and working