Doesn't really matter whether it's before or after IVTC, as long as the frames to be averaged are the same and no other filtering has taken place.
I don't know why are you capturing uncompressed, when a lossless codec would reduce the size of your capture file significantly (I'm guessing about a third of the size you quote).
"NTSC_M_J" sounds correct, and the Proc Amp dialogue is exactly the same as I have with my card. You need to tweak it, because all video sources are slightly different voltages. Make sure the brightness is high enough so that your blacks aren't crunched, and the contrast is low enough so that your whites aren't clipped. The waveform monitor in the colortools VDub plugin is excellent for checking this.
You can also boost the saturation as well if you wish; find a spot with pure red and ensure there is no clipping by using the colortools vectorscope. Leave the hue alone; I messed with it for my original laserdisc capture which unfortunately led to some of the colours getting washed out.
I also put the sharpness right to the top; this is what caused the halos you can see in my LD capture.