On the bottom of your batten pocket, I've had a similar problem and found a small folded piece of tight woven fabric has worked for me to protect from a future puncture. It needs to be small enough to slide all the way down the pocket and especially past any seams. About 2/3rds the pocket width, folded so it won't let the batten slide past is what I did.
On tying the top of the batten, in Hawaii if we tie using Hobie's instruction, we quickly loose a batten. I tie a very ugly but secure series of knots. On a TI, not very tight, AI a bit snugger. I knot on one eyelet, then knot on the batten cap hole, and then the other eyelet. Finally back to the batten cleat, and back to the first eyelet. If any line is left, I knot it around the other lines.
Lastly, on the ripped stitches, I have on older AI sails that I have hand stitched with heavy polyester thread. Turns out better than new, once you figure out the stitch pattern.
- - - - - Hobie Island Sailing since 2006 - - - - - 2011 & 2012 Hobie AIs and a 2012 TI