For tuning, you can swap in a 97 lumina PCM to use HPT. You will loose your second gear start functionality though (I didn't mind). I know Bxx can tune it for you.
Read this to answer a lot of your questions:
You do not have to grind your LIM to make room for the rockers. I recommend using the stock 3100 injectors unless you really want to rewire each one. (thats what I did)
You'll need to buy this EGR adapter to pass emissions:
In all honesty, I ran the entire large port setup including heads on a stock small port 3100 tune and had no issues.