CC top has vanishing belly/waist but only with some bottoms

Well, your rig doesn't have any body parts in it. If you unfold it in the outliner you'll see what I mean. You can fix this two ways: you can either delete the rig and all of its contents then append the rig from your reference mesh; be sure to select all of the body parts listed, as well. Or, delete the rig and all of its contents, save your file and close Blender then open your reference mesh, delete the reference mesh so that only the rig is left, then append your mesh. Either way, you'll end up with a bone_bone_shape and possibly another rig - actually, you have a bone_bone_shape in your scene right now so you'll end up with two.. Just delete them.

Hopefully, this will fix the problem. I didn't see any problems with anything else other than the polycount and some topology issues around the neck and the side seams. 

Edit: Nope. Sorry. Found some weirdness in the armpits. In the UV editor, enable keep UV and edit mode mesh selection in sync. Enter face select; it will automatically switch to face select in the 3D window. In the UV editor, hold shift and hover your mouse over the arm, press L. Still holding shift, use L to select the other arm and the neck - front and back. Press X and delete them. Use L to select the faces in the armpits that belong to the nude top and delete them. Select and delete the waist portion of the nude top. Delete the rig and all of its contents. You should have just your top in your scene and nothing else.

At this point, you may want to clean up the topology around the neck and the side seams. You can merge vertices or dissolve some of them. To merge, shift-select whatever vertices you want merged and press Alt + M. To dissolve, select a vertex, press X > dissolve vertices.

If you want to lower the polycount while preserving the topology, dissolve edges. Alt + shift-select edge loops, press X > dissolve edges.

Save your file. Open the nude top and append your mesh. Delete the bone_bone_shape and the extra rig (if one gets imported). Select the nude top and delete the parts covered by your mesh then join it with your mesh. Double-check the cut number to be sure its there. 

If using a proper rig doesn't fix the problem, and if you're only seeing the problem when using the sliders, it's because of the uv_1. You may need to retransfer it. Use these settings:

That seems really weird that you lost your weight and vertex paint. If you saved your top as a .blend file it should have preserved all that. If you exported it as an .obj then you'd lose your weight and vertex paint. Is that what you did?

And yes, black vertex paint means your mesh won't work with the CAS sliders. The uv_1 is for the sliders and vertex paint is a way to sort of refine how the uv_1 works, if that makes sense. They work hand-in-hand together.

I didn't see any problems with your mesh other than the vertices along the neckline. The neckline needs to be cleaned up. One important step is to put your mesh in object mode and solid shading and pan the camera around. Look for odd spots, places with weird shading. You've got a couple on the neckline. You just need to merge some vertices and perhaps dissolve some. Look for areas with faces squashed between other faces. That can cause ugly shading that will show up in-game, as well.

If it helps, I have a tutorial in my signature. It's mostly a to-do list but it's complete.

Due to gender flexibility many CAS clothing items are made and classified for one gender but appear for both if the fashion choice includes both, with the game automatically morphing the mesh to the opposite gender shape when necessary. The female waist is higher than the male waist, and normally when pairing a made-for-female top with a made-for-male bottom the game also automatically fills in the gap.

In your original package the top was classified as both male and female in the age and gender flags. In this case, with the top classified as male as well as female, it didn't detect the conflict and you got a gap when paired with a made-for-male bottom but no gap when paired with a female bottom. All you needed to fix the gap issue was to classify it as only female.