1. Try to output at higher resolution than 480i, unless the documentary was originally 4:3 SD video. I assume that your DVR recorded in HD resolution.
2. Delogo in VD for removing the logo (there are other similar tools). Here is
my tutorial for removing solid logos and dust spots (same applies to both) using Delogo.
3. 120 minutes on one single-layer, single-sided DVD is pushing things. Even with a $1,000 pro MPEG-2 encoder, you are going to see quite a big of artifacting. 90 minutes is a much better target.
4. Use any of the dozens of bitrate calculators to determine what bitrate to use for any given video (and audio) length. This is a link to my own
bitrate calculator. It works in Excel.