You've been reading the forum, and have some great gear!
Some thoughts from what I've read on the forum. Perhaps you have already read some of this advice in the forum.
MPEG-2 15 mbps is best. Naturally, DVD is limited to about 9 mbps. I haven't made blu-rays myself, but there's plenty on the forum about how blu ray supports an mpeg2 at 480 resolution and this "higher than DVD bit rate". Or if you are not going to disc, Hard Drive space is cheap, so don't skimp on bitrate. Many may argue with you on H264 being better. Mpeg2 can be either interlaced or progressive. Analog video compressed at 15 mbps seems to be pretty good archival quality and a bit of a diminishing returns point beyond that. Mpeg2 is still a broadcast standard. So, it's just that mp4/h264 has taken over with the dominance of the computer/internet domain for video. But in the disc and TV world, Mpeg2 seems the better choice. And with a player like VLC, I don't see why Mpeg2 cannot be played on computers just the same. I understand you won't have a lot of time for restoration when you have 1000 tapes to get through. But something worth noting is that VHS is rather noisy. If you were to denoise the video some (plenty of forum threads on that), you can get more for your bitrate, so to speak. If the video is just encoding he fuzz/noise you see, it will take more bitrate to encode it well. But with the noise reduced/removed, a variable rate encoder wouldn't need as much bitrate to preserve things.
H264 has to be progressive, I believe. There's a lot of sentiment on the forum about not deinterlacing the video to progressive and letting the player deinterlace your video for you. If you are not posting to the web, which often requires mp4 over mpeg2, then I could see why you need H264. Otherwise, the sentiment on the forum seems to favor keeping it interlaced in mpeg2. Naturally, it's your choice. Do it both ways and see what you prefer.
The version of TotalCode Studio I've got has some pre-settings you can start with such as DVD MPEG2 or Blu Ray MPEG2 or H264, etc. Then you can still tweak some settings after that. I don't recall tweaking much for a DVD, other than maximizing the bit rate. Others can chime in with more experience here.
As has been said before, after you trim the edges in post, but before adding a border back in to keep the 720x480 (assuming NTSC) aspect ratio, you can read on the forum how to use avisynth or
virtualdub plugins, along with histograms to optimize the contrast (and also color if you want to spend the time) of the video so that it is not so washed out. Basically, try to get as much histogram coverage as you can so video is not too dark or too bright. Not a universal truth, but usually a good rule of thumb. Naturally, there's also talk on the forum about how you can preview the video before capture in
Virtualdub with the edges cropped off, so you can adjust your brightness/contrast settings in the Levels menu so that you get a good spread of contrast, but without going into the red on the Virtualdub preview histogram with too dark or too bright of video levels. Also, you can use the audio preview to adjust your levels so you capture the audio to something not too quiet and not too loud. I try to set things so that the loudest point in the audio doesn't go beyond -6 db in the preview. Or maybe lower than this. But going higher can get tricky, as you cannot undo clipping of audio, but can always amplify it in Audacity or
Sound Forge. But, of course, remove the video cropping before doing the actual capture. It's not always the case, but sometimes the video in the areas you would crop out after capture can have the darkest or the brightest levels. So, by cropping them out in a preview before capture you can get better capture levels.
Be sure to refer to this
http://www.digitalfaq.com/forum/vide...-settings.html
Your JVC settings seem consistent with many other's advice on the forum.
No experience with ATI MMC. I only capture lossless and use Virtualdub.
Best of luck to you!