Have you already removed the existing metal sunroof panel? If not here's a decent video showing how.

 

 

If you removed the stock panel, installation of the CF replacement sunroof panel should be pretty obvious - goes back in the same way the stock one came out; just bolt it back on with the stock M6 nuts. You may need some shims under the studs/nuts to get the panel to align with the roof properly when closed. Now if your new CF "replacement" panel is just a blank panel, and is missing the 6x M6 mounting studs like the stock panel that are supposed to line up with the holes in the stock panel brackets/trolley, you're going to have to get creative and figure out how to fabricate something.

 

Careful, there used to be a vendor that used a different thread and pitch, cant remember if the studs where american instead of metric; but they weren't the factory thread. To add to what you said, OP be careful when bolting the cf/fg panel, the studs are glued in, make sure you dont over torque them; the studs will come lose, or even fall apart.

 

If water is still getting in then you might have the same problem that plagues most FC owners which is the sunroof bracket (holds the whole sunroof tracks and motor) has become Swiss cheese in appearance and will leak. its designed to drain rain water through 4 sprouts at each corner that have tubes attached to them. i recently went through the trouble of cleaning and repairing mine as I had no luck finding a rust free one. also if your sunroof seal is in good shape would help as well.