I don't know what you're missing. You seem to have it right.
1. All of Nikon's digital cameras have a built in low pass filter that blocks IR to varying degrees. The older bodies like the D1 series and the D2H have less aggressive filters so more of the IR was let through to the sensor. This was a problem to some where things like black fabric had a magenta cast and required an IR blocking filter. This was a serious problem for Leica when they released the M8 digital camera which required adding the IR blocking filter in front of every lens.
2. A deep red IR pass/ visible light blocking filter is required to take IR photos. When added to the front of the lens on a SLR camera body, film or digital, it blocks any view from the viewfinder. You need a tripod and the filter removed to frame the photo before the filter is added and the shutter released.
3. When using this IR filter on the lens and depending on how aggressive the blocking filter is in front of the sensor it can determine if the body can be used at all in the case of recent bodies or how slow a shutter speed and how high an ISO setting is required to get a reasonable exposure. As I recall no matter how long an exposure or high the ISO was set I couldn't get an image at all from the D200. My D1H is fine. I tried a D80 with the R72 filter and it required an exposure at ISO 3200, f5.6 and the exposure bias set to +5 EV. The shutter speed ended up at 1/3 sec for a good exposure in full sun.
4. Now to eliminate the very slow shutter speeds and the viewfinder blocking red filter, you can have the IR filter over the sensor removed and a IR passing filter added. However since infra red focuses at a different point than visible light the AF system in the camera is re-calibrated to IR. The company that removed the old filter and adds the new filter will do this. Nikon's older lenses had red focus dots on the dof ring on where to move the focus after focusing with visible light. That normally meant you had to focus a little closer than what the focus distance scale indicated.
5. So now you have your camera modified with a new filter and the AF calibrated. From here on in taking your photos is just like it was before your camera was modified. You no longer need a filter over the lens. The camera's meter will give you pretty good exposures but in some cases not perfect. Bracketing would be a good practice.
6. The final step after you take your photos is post processing. Your digital images will now look pink. There are a couple of things you need to do. First to get the all white foliage b&w photo you see in so many IR photos you need to de-saturate the image and then bring up the levels to get a nice balanced histogram. You're just about there. A little touch up in exposure or maybe contrast and you've got a nice b&w IR photo.
Or if you want a somewhat false color IR photo you can adjust the colors in the color channels. There are lessons on how to do this. The photos can look quite striking. LifePixel also has different strength IR filters for the sensor that can make this easier to do then with a strong IR filter. It lets some of the visible light through.
And that's about it. I don't know if I've missed anything but if I have I'm sure someone will jump in.