Dan, so good to learn about your successful trans-Atlantic voyage!
I have only sailed my junks inshore, so have never experienced this problem. However, I have always made the batten pockets at the mast from a tougher material than the sail itself. I have used quite thick pvc material; the same as I use on the yard and boom, where they rub on the mast. I would consider to just stitch patches over the longish holes, still with the sail rigged. I would use long (20mm?) stiches (curved needle), as they see little load. When a patch wear through, it will be quick to replace it with another one.
When making new sails for offshore cruising, I would pad the (aluminium) batten with some soft 10mm material, and then make the forward batten pocket roomy enough for this. This should increase the contact surface between battens and mast, and thus reduce wear.
Good luck!
Arne
PS:
As for batten parrels, I soon changed my first 10mm ropes for 20mm webbing, as the latter don't catch each others when hoisting sail.