This is just my 2 cents so don't take it to the bank.
In my opinion there will be more money in your pocket if you can sell the HiPo pieces without the truck. People that are looking for HiPo parts know what they are after and appreciate just that and are willing to pay for it. People that are simply in the market to buy a nice truck don't necessarily appreciate those goodies and just see the truck as having the pieces needed to run. Why should they have to pay a premium to have pieces need to make the truck run?
Virtually no one unless their hands were actually included in the build or know you personally will give you what you have invested lock, stock and barrel in a built vehicle. In fact, many consider this as detrimental as they don't know if the engine has already been pushed too hard and they are inheriting someone else's future problems.
If the parts you pull off are in top-notch shape you could expect 50% to 75% of new value plus the truck will go for what I would assume is a higher book truck on its own merit. Kelly and NADA simply don't account for the add-on pieces on the truck.
If it were me and I was in your shoes, I'd pull the pieces before any potential buyer actually saw them on the truck. That isn't to suggest you would deceive anyone, but buyers want to know the truck runs as an F150 EcoBoost should run, just as it did when new with the OE parts on it.
By the way, one last question, have you gotten the opinion of more than one Tuner as to whether these are your only options?