In Prepar3d. 3.0, I turned off Tessellation and that solved the problem of the 3 second stutter. Time for a new desktop I suppose.

Disabling hardware tessellation and reducing shadow resolution mostly fixes it, but noticed that it still comes back whenever flying into area with large amount of textures. So probably has something to do with video memory. Was keeping hopes on the "reduced gpu memory bandwidth usage" fix of 3.2, unfortunately the stutter still occurs.