So is it this area of the model that you want to fix before slicing it up?

If so, define a ucs along the top surface and and add a box.

union it with the existing solid and use slice and Boolean subtract to trim it. Sometimes slice would post an error that the slice plane did not intersect the solid although it did. In these cases I created a box and used Boolean subtract which did work.
I got to this point in the process and found that one of the surfaces I thought was flat is not flat.

One way to ensure a flat surface is to create a UCS at the orientation that should define the flat surface and then create a polyline starting at the UCS 0,0,0.
The following image shows the 3 points used to define a ucs. The green polyline are the points1, 2, 3, 4 and 5 projected to that plane.

I extruded the green polyline to with a taper of -30° to ensure that the edge surfaces of the extrusion would go beyond the adjacent surfaces while anticipating that they would be trimmed later.

The union of the two solids failed! This leads me to think I should go back to your original geometry and work with the 3d wireframe model before it is given thickness and make sure the 4 surfaces are flat before making the shape a solid.
The image below shows the result of rebuilding the 4 shapes so that they are planar. The shapes were then extruded with a taper of -20° and a thickness of 1. The taper helps to ensure that gaps between extrusion are filled.


At this point we can use slice and Boolean subtract the clean up the geometry. I had much better success with subtract than slice.
Here's the final trimmed shape.


Good night!
lee.minardi