I remember the first Z80 assembler I wrote, about 20 years ago. Back then we had very limited resources (on the computer), so were forced to do a fair amount of work on paper.
The way to identify the construction of the instruction formats is to create a 16x16 grid (for each hex digit in the basic instructions). When you place the instructions on this grid it will become very obvious how the instructions are structured. You'll even see how the designers used a few meaningless instructions (e.g. ld a,a) to find encodings for other instructions (e.g. HALT). Once you've done the basic instructions, overlay the extention opcode tables: you'll find that the IX/IY instructions closely map onto the HL/DE register instructions. You'll also find that you can guess a few "undocumented" instructions in the CB extention set -- there's one empty column, IIRC).
I've sorry I can't remember more of the details: it was a long time ago, and I'm suddenly feeling old.