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From what I have found is the gas motors have a 7 bolt bell housing and the diesel has a 6 bolt pattern. The torque converters for the gas have 4 bolts and the diesel has 6 bolts.
The 6.0L, 5.4L, and 6.8L all have the same bolt pattern. Any transmission that will bolt to one will bolt to either of the other two, also. Having said that, you need to know that there never was a 4R100 mated to a 6.0L from the factory. The 7.3L diesel has a totally different bolt pattern and will not work.
A 6.8L trans will work. It might shift a bit firm because some of the clutches have more plates than a 5.4L trans. I don't remember which ones, that was a long time ago.
Thats what I thought, but wanted to make sure. This truck is the only vehicle I own that is essentially unmodified and I would like to keep it that way if possible. One example is my 94 Bird is a span from 1994-2003 and I have to keep a binder with part numbers so that I remember what I did.
Not sure but it may be programming or updated parts that may have been **** to breaking on 99 & 00 trucks. I dont know alot about transmissions but someone should chime in soon.
I don't know the specifics on every change. I believe all 99-04 4R100s are interchangeable, as long as they are correct with respect to 4x4 or not and engine size.