Mechanically sound, correctly done modifications like you describe, should not lessen the value. Crude, poorly done, and designed by the imaginative day dreamer/cobber would seem to be more of a concern when it comes to value.
If I was looking for a tractor, mechanically sound, in good operating condition, + things like tires and that everything works as it should would be the most important thing. Mine are used for work or to accomplish tasks around the place, so that and the above go hand in hand.
Now if someone overpowered it or just made modifications that would render it useless in the field, I'd more than likely pass on it.
I would certainly enjoy a hundred series ford that was original and complete, reaching even further low hours original owner, shed kept, can't seen anyone not enjoying one of those as is or to restore for light use, shows or to have one just to enjoy that or any other similar way. I still work on my old 850 and keep it in reasonably decent shape and field ready, thought its well worn and still needs much more work, without it, I'd have no firewood put up or get the fields cut, so a tractor that has been modified per what you have done, not being a picky and discerning fool, if the price was fair and the same as others not modified or have replacements that don't make it a numbers matching tractor, I'd pay the same.
My ole 850 was a real mess when I got it but ran good, and as much as I need a much better tractor here, given the work that needs to be done, just cannot afford it on the current salary, and boy have I tried to cure that, only to get to the top 3 candidates for any decent jobs, then I always get cut, worst of that is; "It don't provide no derned better tractor money" LOL!!! So.... I've somehow made it work, its been modified to LP, not very pleasant on the eyes up close, I'll bet I'd not get $2500 for it as is, but even then adding up paying jobs I've done with it, + all the work, firewood and similar things it has done or provided, I'd still not have any loss if I sold it for $2000. Cripes, what you have, when done, will likely be in better shape than what I currently have, would make sense to pay the asking price if fair, without hesitation, I'm probably not the only one in that situation either LOL !!!
Tractor economics 101 ! LOL !