A 1997 3.8 motor from the scrap yard has got about 85k on it. Would it be a good idea to change oil pump and put new main and rod bearings in it.

I wouldnt bother with the bottom end. But, if its a L36, then I would look into changing the lower intake gaskets and replacing the upper intake manifold, plus plugs, and wires

I would consider plastigage measurements of the rod bearings, water pump, aluminum frame LIM gaskets, sleeve for the UIM and reduced diameter stovepipe. I also install a new crankshaft rear seal and make sure the carrier bolts are loctited as a leak from the rear end requires removal of engine or trans to repair once the engine is in the car.