Will the stock yoke in a Ford 1987 f-250 dana 44 adapt to a drive line from a jeep ??? ( XJ , MJ , or YJ ) or will I have to change it out in order to use my Tom woods drive shaft? The same question also applies to the dana 60 I have in the rear.

If the TW shaft has the same sized joints as what the new yoke is made for, then yes. FWIW, D30, D44, D300, and NP231J yokes are all interchangeable depending on u-joint sizes.

Your 60 yoke should be in the same boat, provided the u joints are the same.

At this point, I'm wondering if the fact your axles are from a F250, the ujoint sizes may not match up unless you accounted for that when you ordered your TW shaft...