FWIW I like cropping/re-sizing in V/Dub or AviSynth better, tending to use those much more often. Using Vegas I've had good luck cropping/re-sizing first in AviSynth, then feeding that to the time line via VFAPI. In Vegas itself, the problem you might encounter is Vegas wanting to render the cropped &/or re-sized clip more than once -- if there were 3 re-size operations for example, 1 to match the project, 1 after you adjusted the frame, & 1 to render, instead of just going to the final size from the original, I've had it perform each step internally.
That said, for what you're after [unless the 6 pixels contain garbage] I'd probably just re-size since the 6 pixels are well within the tolerance most everyone uses today [just watch cable]. If you needed to crop just as you've said turn off the aspect in pan/crop, as well as adjust from center turned off, with the project set to the final video. If the crop was symmetrical you could set your project to your D1, then cut the size on render/encoding -- it's most always good to send the encoder all the data you have to work with.
You may need to trim the left and the right edges.
In Compressor, you just specify how many pixels, if any, you want to trim off the top, bottom, left, and right edges when rendering.
That's as clear as it gets, but most MPEG-2 codecs will interpret 720x486 D1 (8-bit) or 720x486 D5 (10-bit) correctly and render out 720x480 with the top 4 and bottom 2 lines not participating in the render.
The footage was ingested in a Media 100 machine. The footage was shot on Beta SP (I think). I copied the files to an external hard drive and now what to work with them inside Sony Vegas.
You must be using a newer version of Media100 than I've ever used. Last I tried it, M100's codec was proprietary. But it's been several years.
The problem, I think, is that Vegas doesn't give you any control of the crop when you render directly from Vegas. Since the SDI capture from M100 leaves 4 lines of black at the top and two two at the bottom, Vegas needs to be able to crop those. Instead, I think Vegas will crop three and three when you render and that's not what you need. Here are some options.
Option One:
First, edit the footage in an NTSC Standard 720x486 template, then send the finished output to a third party renderer like Compressor (which has more control of how you crop the render). This will require that you render or frameserve from Vegas before you can get it into Compressor. It also requires buying Compressor or ProCoder, or maybe just using Vdub.
Option Two:
Edit the project using an NTSC Standard template. Use the finished output in a new Vegas project using an NTSC DV template. "Finished output" could be frameserver output from the first project to the second, or the first project could be nested in the second, or you could render out the first project and drop that rendered file into the second.
The goal here is to do all your cropping and nudging in the second project. This sounds like more work than option one but it's really pretty much the same procedure. Once it's in the second project you can pan/crop the event to get things right.
Option Three:
You could set up your Pan/Crop in the initial project but to my way of thinking the first two options are more likely to isolate any problems you may have, and the editing will go a little faster if you don't have pan/crop running.
As always, test things before going too far down any road, especially since all my ideas are off the top of my head and might be wrong in some major detail.