An 89 is past the disintegrating wiring harness, that's a good thing.

Trans problems can be pricey/time consuming, even if it's just putting in a used one. The AW transmissions usually last a good 300,000 miles if cared for.
Low fluid may mean it wasn't cared for.

If you mean the pinion seal as the output shaft seal of the trans, then I hear it's a fairly easy job overall. Also, I'll second that the filter doesn't need to be changed. The filter is about as fine as a window screen - just metal mesh.
If it's in the axle, that one is beyond me to answer.

I think a new windshield seal should be doable at a windshield shop for about $100.

The 89 maaaaay have OBD1, but I wouldn't bet on it. I think the models made late late in 89.

The speedo not going over 55.... That sounds like cluster problems. That's one for other people.

Sounds like you're getting what you pay for.

Cheers!
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1990 740 Turbo, on its way to stock specs, maybe beyond