I'm don't really have the necessary experience and knowledge to offer adequate WED tips, but I'll give it a shot anyway.
*Snap all block geometry to the grid.
*Do not overlap, snap instead.
*Do not create planes (blocks) thinner than 2 quants.
*Move the faces and vertices yourself. Try not to use CSG Subtract.
*If possible, instead of using holes or null spaces,
---use textures to simulate static portals (windows, doors ).
---There appears to be a fair amount of holes/null space in your level.
---Using textures instead, may increase performance significantly.
*If accurate lighting isn't truly necessary,
---you can compile components/rooms separately to map entities
---to save time on compiling.
---Select the faces of the component and click "finish".
---Save the .wmp geometry group for the map component.
---To open the file in another instance of WED,
---double-click the .wmp map geometry component just saved.
---Compile to map entity in the other instance of WED.
---Close the other instance of WED.
---Return to the first instance of WED which contains the main level.
---Add the map entity just compiled.
---Line the map entity up with its uncompiled duplicate geometry
---in the main level.
---Delete the uncompiled duplicate geometry in the main level.
To reduce compile time use "flat" instead of "shaded".