I think the minor mods for the factory make no difference as its something that is correct and makes it more user friendly.

To me the engine conversion is easily reversed if you were to sell it but it would be important to keep the original to go with it if you sold it. The engine conversion is a thing that would maybe turn me off. I fully appreciate why you would do it though! Better if it was a 308 to start with as there would be no obvious difference then until you drove it.

All the other things are no problem really, except if I found a tuxedo black one that would be a major bonus. Love black cars even if they are the worst for a million reasons. (You should see the paint on our black prado after 100000km! Not very nice.)

Depends why you are building it really. If you are building it to keep, why worry about your plans, and if you are going to sell it you can easily test the market and if it wont pull the dollars you reckon its worth put it back to standard.