Dan,
You have every right to be frustrated and annoyed with Hobby Design but that won't fix the photoetch and neither will they. You might consider pieces of shim brass in between each layer to build it up to proper height.
K&S Engineering sell a pile of assorted sizes of shim stock for about $3.00 (US). Sizes include .001", .002", .003", .005" etc.
Example: (14) x (.003in) x (25.4mm/in) = 1.07mm.
If your hobby dealer doesn't stock K&S you could try a local machine shop. They use shim stock to adjust for wear on their machines.
Good luck with the build. I'd like to do this one also so I'll be watching.