I don't see why considering it's a clone, since you will be putting it like "TM.com Clone" it's not affiliating you or the company with eachother. You could ask whether a 'We are not affiliated with TM.com' at your footer would be acceptable, if not, remove anything you say about TM.com (rename the script) and change the design if you've copied there design as well.

Also I may add, the Digital Millennium Copyright Act of 1998 is a USA law so it shouldn't be a problem but as for the trademark voilation the EU has it's own trademark laws - I recall the EU asking about an agreement between the USA and the EU but I'm not sure whether they have a trademark agreement - since the notice was sent under the DMCA it is most likely the trademark is registered in the EU.