Do both? I haven't voted, though.
Becasue, it's not quite both.
Get the Cannondale, and then get the custom *frame* done. Likley the custom will take some time, but it will be worth the wait and perfect forever (especially if steel or Ti). Use the Cannondale in between the time you order the custom and actually get it.
Then transfer the bits over to the custom. Keep or sell the Cannondale as you see fit. That way you also won't be breaking the condition of the Cannondale sale to you.
Whichever way you go, make sure the Cannondale fits. As a by-the-by, the new blue paintjob on the Cannondale tourer I have seen seems nice, but what the heck is that unintelligible logo they've got plastered all over the top and down tubes**********