This forum has a search function. Use it right and you will find plenty of EMB info.
But I'm feeling nice so I'll point you in the right direction. Also you do not need autotune.
You'll need to get a copy of GReddy's tuning software for it. Don't waste your time with the "alpha tools" if you run across it. You should be able to find the software and manuals on this forum: http://diytuning.com/
. If not I know I have a copy of it somewhere so just let me know.
You're going to need to get the wiring diagram for your 2004 ecu and go from there. If you don't want to hack up your stock harness (I wouldn't) you can get an adapter harness from boomslang.us. Also I have a semi-hacked up harness for my '97 with an o2 clamp and GM 3 bar MAP sensor I could sell you. All NA/NB miatas use the same N76 connector so you'd just have to swap some wires around.
The above mentioned o2 clamp is used to trick the stock ecu into thinking that AFRs are stoich when you're in boost so it doesn't try to pull the extra fuel you're adding in. The MAP sensor is not required but it's easier to tune off of, especially if you're planning on running 12psi+ like I did when I had my EMB setup.
The EMB can compensate completely up to around 400cc injectors on the miata (basically 150% stock). If you plan on using stock injectors and running more than 8ish psi you'll need an AFPR (also got one of those for sale haha).
Should be a good start for you.