A couple thoughts: What type of 3D printing are you using? Stereolithography might be something to look into. It uses a laser to cure liquid resin. I know there are a few different flexible materials you can get. It'll help solve the layer adhesion problem that FDM usually has. It also will stop the stringey-ness that you get from FDM.
Deepening on how much interest this is getting, it could be worth it to go with injection molding. It's more of a cost upfront but the materials are endless and you can manufacture perfect reproductions.
Silicone mold would be best based on quantity, you will also get the best quality i think.
That does look pretty good and once it’s tightened down it would provide a good seal. Does the edge of the rubber bulge whe it’s clamped down? It’s tough to tell from the pictures.