You already mentioned that the car doesn't have the original engine, so you've already taken any hit on the value that the original drive train would have brought. But, keep in mind that some people value numbers match and others don't care in the least, the latter is the group that you'll be dealing with if you ever decide to sell the car. So, since the original drive train value is already gone, changing the transmission will have little, to no, further impact. Now there are two ways to look at this, manual trans cars seem to be more coveted than their auto-trans counterparts, so changing to a manual trans may add value. However, as most of us get older it becomes more difficult to manipulate a clutch pedal, so the people that maybe had a knee replacement, or their legs just aren't what they were when they were younger, may begrudgingly be drawn towards an auto trans these days, so the auto might add value to an aging crowd, but not because it's correct for the car.
In the end, it's your car, so do what you want. You can always keep all of the parts that you swapped over so that any future owner, or yourself, can easily swap it back and they'll have the correct trans for the car.
These are just my thoughts of course.
