Isolate each layer, then Select All, convert strokes to outlines, select all click on Merge in Pathfinder, then Trim in Pathfinder. This should isolate every single item on your page irrespective of if it was in a group, compound path or clipping mask.
Now, when you ran Merge and Trim Illy creates additional clear and/or white fills [I don't know why] where there was white or clear previously, you need to clear those for the next step - sometimes they are white, sometimes clear, sometimes 0% black - again I'm not sure why. You need to look for them in preview (ctrl-Y) - they'll be lines where you are expecting none - select one of them, select same fill color, delete...
Select All, then Unite in Pathfinder. Volia!* Repeat for each layer. (If youwant to "merge" the whole doc, have all layers visible.
You might be able to do that last step with the Shape Builder tool, but I'm not proficient in that yet, doesn't always do what I expect / want.
Are you sure that what you are seeing are 80 separate layers rather than one layer with 80 sublayers? In Illustrator every new object added on a layer becomes a sublayer. If this is the case for you then try selecting one of the five complex objects you mentioned. You'll note in the screen shot that the selected objects will have a solid square showing at the right of the sublayer. If you choose all of the layers with a solid square next to them you can then drag them all to a new layer that you've created in the layers panel by clicking on the square with a + sign in it from the bottom right of the panel. By repeating this for all of your complex objects you can wind up with five layers each containing only the appropriate sublayers.