Any pictures? What's the spec of the engine you've built, as its a zetec turbo I'm guessing?

There should be a deeper sound as you've opened up the exhaust passage a lot more than standard. So think of it as if you've just made one whole exhaust without any baffles....

Try dissconnecting the battery, leaving for a while, then reconnect and allow the ECU to relearn all of the parts it has fitted to the engine. Same principal as the Focus RS really...