I'm assuming you mean from the engine running, like if you leave it idling and step outside you can hear a tick from the engine? Does it go up consistently with RPM? If thats the case check all your header bolts and make sure none have backed-out. If the tick is really actually coming from under the car, check the flanges at the header/mid-pipe and make sure they are nice and tight. Also make sure the rest of the exhaust isn't hitting the body at any place (but that usually makes more of a rattling sound).
Lastly, has this occurred ever since you did the head swap or just out of the blue? I often hear of improper pushrod length and valvetrain geometry issues associated with TW heads...