That's a somewhat convoluted workflow. I'd say you've left yourself open for a lot of unnecessary work -- and specifically, you should be aware that lossy encoding (MPEG, h264, etc.) is lossy, period. Each re-encode loses more data from the original, and it's data that can't be retrieved later. If the DVD recorder gives you cleaner captures, why use the Shuttle? As it is, no one here recommends that capture device for VHS. You can record directly to the DVD recorder (not the best way, but likely OK if you use a very high bitrate) and transfer that recording to your computer as a 1:1 copy.
Lordsmurf has the right idea. Since the last step in your workflow is deinterlacing and re-encoding for streaming, you can avoid a lot of image loss and audio sync problems by capturing with an ATI USB device to lossless huffyuv
-- which means one and only one encode as the last step. ATI and Hauppaugue ATI-style USB devices are discussed in a number of threads here, and drivers are available for different versions of Windows in this forum. I'd also take lordsmurf's advice about Premiere. It's fine for editing and other corrections with lossless media, but you can get better h264 or MPEG encoders for much less than the cost of Premiere, including many good free ones.
This forum has hundreds of threads dealing with proper and better methods for digitizing VHS. The methods you suggest will look no better then the original tapes, and probably somewhat worse.
You did mention that your MPEG captures look OK to you, which is an odd statement because at the same time you state that you don't know what you're looking for. If you can provide a short 10 seconds or so of a capture, many members here can help you with that. If you don't know how to make a short MPEG sample without re-processing what you cut out, let us know. There's a lot of free and simple software around that can do it.