I have created a sub domain ipv6.jtn.org.uk which has AAAA record pointing to my server on 2001:470:1f09:697::1
Your forward DNS is working. But there are two details you should be aware of. Resolving the domain requires a few more requests to authoritative DNS servers than a typical domain due to using NS records in a different domain which have to be resolved separately, and those records themselves rely on NS records in a third domain. Additionally the DNS servers are IPv4 only. That of course doesn't stop them handing out the IPv6 address of your server.
When doing reverse DNS the resolution ends at the HE DNS servers, which respond with NXDOMAIN. I tested that step with
dig +norecurse -x 2001:470:1f09:697::1 @NS1.HE.NET.
The DNS servers used for your forward records don't consider themselves to be authoritative for the reverse zone. When I try to send a reverse lookup to them, they refer me back to the root. I tested that step with
dig +norecurse -x 2001:470:1f09:697::1 @79.170.40.2
Thanks for your help, I can always use another domain and use HE free dns service which might be simpler but either way I'd like to see how this domain goes first.
You don't need to use a different domain in order to use HE for the reverse lookups. All you have to do is to go to the HE DNS configuration and enter the reverse records. It doesn't get simpler than that.
You can also go with another DNS provider (which could be the one you use for forward DNS or a third provider). In that case you first have to register the reverse zone with that provider, then create a reverse record on their DNS server and also go to the tunnelbroker configuration page and point reverse DNS at the provider you chose.