By clone, do you mean going the whole nine yards and converting all of the trim to "cuda" trim or are you just talking about putting a 440 in and leaving the gran coupe trim?
I have two gran coupes, a 70 and a 71. The 71 is a non matching #'s car so I converted it to a 340 4-speed cuda with a shaker hood. I've been offered lots of money for it since the conversion and no one would even stop to look at it at a car show when it was stock. As for the 70, it's a matching numbers 318, but I'm building it for my son and he will not drive a 318 car. We're going to build something different with this one. We have a 340 six pack motor and a 4-speed setup. We'll use an AAR hood (painted to match), no gran coupe or cuda names. Rear tail panel cuda moldings, AAR rear deck spoiler (painted to match), leather interior, full front spoiler (painted to match) and the color and wheel choice are undecided. Was planning to go silver until Troy built the Sickfish. We may use the 18" billet 500's like the ones going on my superbird clone.
My opinion, and I own and have built a lot of cars, is to build the car to suit yourself. The market value of the car is absolutely not important. What is important is what makes you happy when you walk into the garage and look at the car. You need to decide what it is that you like when you look at other cudas. Make a list of all of the things that you like about those cars. While a 440 is killer, I personally enjoy driving my 71 with the 340 in it. My son drives a lot of my cars including the big block cars and he enjoys the small blocks more as well. They drive better all of the way around and don't require the frequent stops at the gas station. My wife's fuel injected cuda gets 25 mpg and my 340 4-speed gets 17 mpg. None of my big block cars come close. Since we drive our cars a lot, including to car shows that are hundreds of miles away, it really makes a difference in how much money we spend on fuel costs in a years time.
Just pull the 318 and store it safely away. If the day comes that you need to sell the car, you will have the matching numbers motor, so no value has been lost.