A good friend of mine just completed converting a 1966 Mustang
HT into a convertible. After reinforcing and boxing up several areas around the rocker panels and center floor boards, he literally cut the roof off - cutting the front windshield pillars off at the factory roof seams.
The absolute best way to do this is to find yourself a convertible donor car - regardless of condition - because proper alignment and placement of many of the components and items such as the front windshield header are a real time saver when it comes to final assembly and a donor car is the perfect template as well as an excellent source for many parts.
Unless your car is a numbers matching Mustang with a K code engine - I say go for it.
It's a lot of work, but there's a lot of satisfaction in the finished project also - and it makes for a lot of conversation with other car enthusiasts.