This first document is a wonderfully complete and highly readable roadmap of the decisions you face as you dream up and flesh out your new architecture.
Creating Embedded Microcontrollers (Programmable State Machines), by Ken Chapman of Xilinx.

And here are a handful of pdf documents posted by Bruce Jacob of the University of Maryland. I've not been through them all but again the readability is high, despite the fact some of the topic material is non-trivial (eg: out-of-order execution).
The RiSC-16 Architecture

This page is devoted to the 16-bit Ridiculously Simple Computer (RiSC-16), a teaching ISA used by Prof. Bruce L. Jacob at the University of Maryland. The computer is based on the Little Computer (LC-896) developed by Peter Chen at the University of Michigan.

The following notes are extracted from two classes:

ENEE 350 - Computer Organization
ENEE 646 - Digital Computer Design