If yours spun or otherwise damaged the female part (output spline) on the transfer case, I would replace that in addition to the shaft with the longer spline.

When mine started to get noisy, I found a good used transfer case, put a new chain and seals on it for good luck, and am using that with the drive shaft with the longer splines.

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David.X5
2001 X5 4.4i Sport
SOLD! at 160k miles