Jerry, first of all congratulations for this project; because it's interesting, and you needed it to distract a bit from the other one - you know it, I know it!
One thing: do you mean the R2 DVD, right? Because R4 (usually from Australia) is PAL... or is your R4 NTSC? If so, from which country is it?
Well, I will be very interested in it, and happy you decided to use a grain plate to improve the quality of the HDTV parts; also, it is a good idea to stick with the audio track as reference, so you have to not re-encode it; even if it will be 10 frames lost, I bet they are all at scene change, and so not too important.
I have both AC3 and DS laserdisc versions, but frankly I don't know if they are different from the DVD...
BD authoring: you know my "policy" (^^,) I like to release BD compliant discs, so if you have some spare time, I strongly suggest to use MultiAVCHD; it's free, and could make also menus; if few days you will be able to discover all its functions, and it worth the time!