berghaus,are you on the EastsideVW forum in Aberdeen?
There are members on there with plenty of horror stories about Speccy cars and won't go near them.
If it's a case of them stuffing up on your car and then using the modfied excuse, then as has been said, take it to WP or get on Eastside and they'll soon recommend you a list of reputable places to go and get a second opinion.
Then go back to specialist and tell them (politely) what you think of their service and the problems it has caused for you and see if they will do a goodwill gesture in paying for the remedial work needed to get the car runing correctly.
Modded or not,if the techs in the workshop know the VW product,then they should have the ability to rectify problems.