I wouldn't worry about messing with the 9th injector. I unplugged mine but that was because I burned a chip that used a later ECM file, which cylcles all the injectors for startup. With my old programming I found the 9th injector to help on cold days however. Just run it as you usually would.
Block off the egr if you aren't going to be running emmisions equipment. Eliminiating the smog pump isn't much of a big deal. You might benefit from a chip reworking after the pump is gone, but Id wait to get the chip done until you are setup with the equipment you want to run.
I run my vacuum ports as follows. The main outlet on the driver side rear of the plenum I run to my vacuum booster. The small nipple on the passenger side rear I "T" off into two lines. One I run to the little nipple in the under side of the Throttle body, the other goes to my fuel pressure regulator. The larger nipple in the passenger rear of the plenum I use for my modulator for the transmission.
Like I have been saying, get a book for the car you are taking the TPI from. You WILL want it and NEED it eventually. If you cant afford the book you cant afford the TPI swap
. The swap ended up costing me about double what I had planned. You might get away with less as you will have all of us (and a good book right?) as resources.