Hi Monsoon, I misread your earlier post.
Difficult situation and really, given the levels of potential tax involved, you should get good tax advice as well as legal advice in a combined effort.
I can see at least four possibilities here:
1. You deal with the transfer of land now in a straightforward deed of partition and pay your taxes.
2. You just deal with the transfer of the site by way of a deed of partition and rectification. Although you do not qualify for the 'parent to child site transfer' relief on the strict facts, you can make a case to the revenue commissioners that this is a deed of 'rectification' and that it should have been done back in 2002, that if it had been done then that you would have qualified for the relief, give them an affidavit confirming that you paid for the building of the house yourself and that your father did not contribute and basically try to claim the relief. I have done this in similar ( although not exactly the same) circumstances for a client successfully.
3. If the intention at the time of purchase was that you would be the eventual owner and your father only became a tenant in common in order to obtain funding for the purchase ( I'm not sure this fits your facts), then you could now have him execute a declaration of trust, stating that he held only in trust for you, that you provided all the purchase monies or repaid same to him and that he never held a beneficial interest in the property and then do a deed of partition transferring all his interest to you. This would then be free of CGT and stamp duty IF the revenue agree the position.
4. Do nothing now or again remortgage in your joint names and wait to inherit your fathers interest. Inheritances are free of stamp duty and CGT but not CAT. However you can show that you built the house from your own funds etc to offset against any potential CAT.
These are some ideas I am throwing out, you understand, you still need good tax and legal advice.