I'm a layman, but from what I gather the go-ipfs to js-ipfs problem is related to the two systems not being bridged 100% yet.
When I added the go-ipfs machine as a 'Bootstrap' for the js-ipfs config it was able to relay the pubsub correctly. Not an elegant solution, but maybe it can be worked with until something better? Even when the go-ipfs pubsub worked, it wasn't that friendly of an output for me. Perhaps nodejs tools using jsipfs are a better route?
Trying to pubsub with the jsipfs binary gives me a 'An internal server error occurred' so my backup suggestion has likely failed before it begins, and here we are.