Notching the towers is a band aid approach to the width issue. You need to get rid of the towers and front suspension all together............unless you are building a drag car.
As was mentioned Rod&Custom makes an excellent kit with everything you need. You can also strip a 94/05 Mustang front sub frame and install it in place of your stock front end.
Good article to read;
The Mustang Shop - How to swap a 4.6l modular engine into an early Mustang
Or give these people a call as he makes motor mounts for the 4.6l to go in a 67/68............don't know much about this product although he must have the information you are looking for.