As you can imagine the situation is very complex.
Lets first deal with the reopening to Port Harbour - due to a dispute with the Trunk Roads Authority, extra embankment work and the WHHR only rebuilding half the line to Pont Croesor and not funding the bridges (or track materials?) there wasnt the money to pay for the expensive LC installations.
However, as it was decided that the NR/WHR crossing would be designed to work with ERTMS, not RETB, opening before 2011 wouldnt have been possible anyway.
Moving onto the WHHR. Simplified, they agreed in the 98 agreement to the FR using their 'heritage train' to run a shuttle service on the WHR. They would've received a fee for the stock and volunteer crew plus a percentage of traffic receipts over the section of line they built.
Their current working proposal however is quite different - they would run a shuttle from their terminus to Pont Croesor and pay the F&WHR a track access charge. There are many issues with this, but most importantly (with Pont C now having a popular RSPB centre) this would act as competition with the F&WHR services as the fares would likely undercut them. However, even if fares were agreed the signalling will not allow such a service until ETS is installed which will not happen any time soon.
I suspect any way forward will be along the lines of that originally agreed to, however when the WHHR were offered the chance to run a Bedd-Port H shuttle a few years ago they declined so progress seems unlikely - for now at least.
Chris