I finally got the shaft out, and this was a bit of a pain--but not too bad.

A bearing puller is a must, and I suggest using the bigger one of the two to get an adequate bite on the shaft. Once I set it up, I used the bolt to push on the very last threads and inched it out until it was out just enough. This seemed to work pretty decently. The inner splines to the transmission were completely fine and even had some trans oil in them.

I suggest orientating the bearing puller like this as it will bite harder on the shaft with the raised up splines. Notice the black dust cover towards the trans input. This thing just keeps large debris out and such.

Notice up close this is a ZF component--obviously as the transmission is a ZF. The output splines are rolled over and was completely caked in rust. There is a heat treatment ONLY towards the inner splines of the shaft. If you look closely, you'll see the color ring with dark blue-ish tint. This makes me think the output splines are not heat treated I guess... -_-
We'll see once I get the new replacement and how it looks for comparison.

The inscribed P/N is: ZF 1069 304 059

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2003 BMW X5 3.0i -- MT5, 3.64s final gears, H&R lowering springs, K-Mac bushing kit
2007 BMW X3 3.0Si -- MT6