It has been said already; A car retains the most value when kept in stock condition, especially with something as valuable as a TA Challenger.
Hagarity says it best in their evaluation estimates "color makes a big difference in car Values" when measured against their proprietary values.
It is true that green is less popular generally when buyers bid on cars at the auctions. If it were me, I would go back to the stock color.
You also spent time seeking out a correct TA motor and trans to install. This will help with the car's value, though an original motor always boosts a car's price.
It really is about what is important to you. You could install the TA motor, and drive it with the non-original color and have some fun. You could change the color and enjoy it, but selling her down the line; you need to find a buyer ok with the color change.
At this stage, I would just build it the way you want it and enjoy.
Keep in mind that very few people recover monies put into a vehicle when they sell. If you keep it long term, that will matter less. Best of luck with whatever you decide!