Why don't you play dumb and go the usual route. When it comes time to pay money you then go and tell them it has already been registered and no fee is due, be argumentative and tell them if you are to leave the office without your logbook/registration cert that you want a headed letter explaining the reason for you have English plates on your car and no up to date Irish motor tax. That puts the ball back in their court and makes them look bad so will make them more likely to help you along.

Civil servants are like obstinate sheep, you have to herd them in the direction you need them to go. Best of luck with your "new" car, I'd say its good to have it back!

Other option is to send your V5 to shannon via registered post with a letter explaining to them what you want done and keep a copy in the car with you for checkpoints etc.