Hey Aussie, I am incredibly moved by your story. I've got 2 kids, 13 and a 15 years. I was also raised with 1 JW parent, one opposed.
It sounds like you have done a great job "planting the seeds" so to speak, just by existing you provide an alternative, a link to the world beyond the org.
I would say your greatest power comes from just being a dad, if you know what I mean? This is what your wife is most afraid of. Sounds like your son is the typical teen, we don't see much of our son either!!!
I have noticed between my son & husband.....they are close, but my son is often very worried about letting his dad down, he interprets his dads advice as criticism.
My husband has no idea of the impact of his words, he only wants to help, I often need to mediate between them.
Maybe this is a natural part of child development, I don't know, but I think that it would be quite easy to drive a wedge between them at this stage in their lives. I'm not saying this is your situation, it's just something I've observed in my house, and from what I hear, a number of my sons friends have similar clashes.
What I do with my 13 year old daughter? In no particular order:
Swim, ice skate, bush walk, pedicure & manicure ( you go too! they will love having a man there, the massage chairs are divine!), high tea, snorkeling, bike riding, botanical gardens, colour run ( search the run guide on the net, they are on all year round, cheap & no age limits :) at least in NSW), yoga ( really good for future stress ), volunteer to walk dogs at dog shelter, art galleries & museums, fruit picking (open to the public days)
My husband also lets my daughter paint his nails....she loves this and spends ages designing something crazy. They also work together in the garage, they have made a dolls house, clothes racks, props for school plays ...lots of stuff. I forgot, my husband takes my daughter fishing, she loves it. She would love to ride horses, but, where we are it's too expensive, I know some places it's really cheap and a great option. Good independent book shops often run a range of kid themed events, get on their emailing lists...they have some great things.
I really hope for the best for you & your family, your kids sound great, they will be OK & so will you! Don't forget to look after yourself....you are a great dad and they are lucky to have you....