KLE can get key placement, then you need to take that to Swill's case and plate builder.
http://builder.swillkb.com/This will give you the cad file you need to cut the plate.
The only way to get what you want is with a universal plate (this includes what you will get from Swill's tool) and those do not fit into the Tex or Vortex case because they are flat while the Filco plate has bent edges. On the aftermarket aluminum case those bent edges are what hold the plate in place. It works really, really well, but it means you need a bent edge plate and I have never seen one offered.
That isn't to say what you want is impossible.
If you have a pattern, you could hog out the Filco plate, while this sounds easier at first unless you have some decent metal working skills/equipment it could be a long process, the plate isn't super hard or thick, but it's not soft and thin either. On the other hand, you may just have to expand the existing slots.
Your other choice is with a universal plate (bought or have made), you just need to a new way to prop the pcb up (not recommended!) or make some adapters to replicate the bent edges. I was making adapters on my 3d printer and sold a few sets but at least one person made them out of pencils(?). I haven't made them in a long time, but the thread may give you some ideas. If you can't figure out a solution let me know and we can try to figure something out.
https://geekhack.org/index.php?topic=45739.0One other problem, and I'm working blind on this so it may or may not be an issue, but universal plates allow opening of MX housings without desoldering, this is accomplished by cutting wider openings, which is where Alps and/or SMK switches clamp the plate.
This plate should work, they don't say what it is made for but will fit the switches and looks like a Filco pattern which is kind of the default. This plate ensures the switches and the stabs you want will work, but still has the problem of a lack of bent edges. It's also sold out so the plate builder may be your best bet.
Here is a picture of the Filco plate vs a universal plate to show the problem.
Photo by WhiteFireDragon, from
here.