Is there a difference between the stock turbo of the 86-88 models, and the 89-92 models?

 

Yes, they have completely different exhuast housings and manifolds. The 86-88 had a twin-scroll system in the manifold to improve spool-up. The 89-91 ditched this set-up and had a much bigger double wastegate.
However the compressor wheel, compressor housing, turbine wheel, centre core and wastegate actuator are identical.
As long as you have the manifold, the turbos are easily interchangeable.