With MSnS, you will use your own laptop to tune. It can even be one of those $75 cheap-o laptops off eBay a lot of the time, so you don't have to have a top-o-the-line lappy to use this system.

For emissions, if you have the ECU disconnected from the injector harness, then you'll get a CEL for injector failure. I've heard of some people leaving the stock injectors connected to the stock harness and tucked away behind the intake manidfold so the ECU can still operate them. I don't know how their running dry will affect them, but it's an idea. The other alternative, and what I had done for my car when I was planning on running MSnS, was to source another injector harness from a parts car that I could wire into my MS harness. That way, I could swap the connection controlling the injectors; MS or ECU.

Emissions/inspection considerations include deciding where you will intall your secondary IAT and CLT sensors. I put my IAT into the hole where the EGR pipe enters the back of the intake manifold. Now I have about three months to find another damn EGR pipe and figure out how to bolt it back up to that location. (I can remove my IAT since I'm not running MSnS, but if you want to avoid this situation, you might want another location for this MS sensor. Besides, I hear flow at this location is less than ideal.)

The wideband is definitely the way to go. MSnS can be set up, as far as I remember, to adjust fuel delivery on the fly in order to achieve preset AFR values. Given temperature and altitude changes, this sounds like a good option to have. Give yourself some time to iron out your AFR and then begin to play with spark.

I think this would be a great place to get started. Get up into the engine management forum and start reading up on what people are doing. You'll pick it up pretty quick.