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Trans Swapping 4r70w to 4r100 any suggestions??

Last year, got my hands on two Expeditions..98 4.6L xlt and a 99 5.4L eddie baurer (sorry if spelled wrong). The 4.6 had a hole in the block, so we used the 5.4, keeping the 4.6 components. Ran great, no problems...until a month ago when the trans fried. Got a hold of a 2002 Expedition trans, but the problem is that's supposed to be 4r100 and basically everyone is saying that wont work if you were running the 4r70w (which that's what fried). Now, say that my mechanic (husband) fabricated the 4r100 to connect in, which he did. Everything bolted up, changed the harness so the trans connects. There's little things here and there that are being address...cross member, shift cable..we can deal with that. Problem is, trucks not wanting to shift correctly. Heard we should use the 02 computer, can't do that. Does anyone have any suggestions, we're running out of ideas!!! What about the speed sensors?
 

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