Instead of "custom", look at "customized". Look at
www.polycase.com.
Tooling isn't too bad.
They use a router bit to make all of the holes and cutouts, so remember no square corners.
They can print, but when you look at some of their drawings with a label area, the printing has to be a little less than the edges. everyone usually wants a vecorized drawing. I had a label printed at a local sign shop - $30 each. I can do an 8.5 x 11 sheet cold laminated for $3.00 in materials. The punches are consumables, though.
I experimented with laser printinng my own labels with round holes with very good results.
I found some nice stock which can be laser printed and some clear that can be cold laminated.
There is a flat paperpath that I can use in my printer. I did the holes with medical biopsy punches. I need 9 holes of one size and 1 of another.
Cutom labes are an option, but tooling is higher.