According to the existing market, you are affecting the value. There are people who may pay the same price and even a little more if the rest of the car is in great shape but I would think only one out of 25 would pay the same or more over a car with a good working original motor in it.
Other than value, it is not an easy question to answer. A lot depends on what you are going to do with the car and if you have someone in the family who will continue on with the car if you no longer can use the car.
If you are going to drive the car on road rallies, tours and afternoon and weekend gatherings driving maybe 1500 to 3000 miles a year, then what you are considering might be worth it.
If you are going to enjoy it for a couple of years and sell it, no, I would not build the new motor.
As a long term usable car, I like the idea of two motors.
Parts and engines are not getting any cheaper.
Many parts are interchangeable.
Being able to drive the heck out of the new engine knowing you have to original on a stand is something to like but-------that usually works if are going to use the car, your family knows where the extra engine goes and even better, you have a family member who will take over as new owner. If you do not have the three items set---I would rebuild the original engine with internal upgrades. Good luck
