Can someone give me the link to that program and can you also answer me this: If I used that program about half way into my mod and I want to use it now (because 50% of my dialogues still lack that generic lyp sync and silent mp3) will there be any issues or should I delete all the files regarding that and make a fresh batch?

http://www.tesnexus.com/downloads/file.php?id=16622 is an OBSE plugin that dynamically uses an 8-second silent voice file and its corresponding lip-sync animation whenever there is no voice file provided. It installs independent of your mod, so it doesn't matter when you start or stop using using it. She's not maintaining it, but it just works and should continue to do so, as there's really nothing to break.

Note that it doesn't generate a silent mp3, it just uses the same one for all those "missing voice file" situations.

So, if I were to submit a mod would I have to include the silent mp3 files and the lyp sync files or could I just tell people to download this mod to save time on uploading and future downloading? Anybody have an opinion on this?

The normal procedure is to just tell people to load the other mod if they find the dialog is going by too fast, which it probably will without the silent voice files. Oblivion determines how long to display the subtitles based on the length of the mp3 files, so Elys' plugin plays an 8 second silent mp3 file to guarantee the dialog is displayed long enough. You could include a link to the mod download page if you want - especially for one as stable as Elys. Normally you shouldn't include another mod in yours because that locks the version to the one you supplied, so if the original author does do an update, your mod won't have it. People typically don't like you including another mod in yours without permission anyways.

Another option would be to try creating your own silent mp3's, but I've read some posts that suggests that's pretty tricky, so just using Elys is probably the best way to go.

I believe TES4Gecko is the program you're looking for: http://www.tesnexus.com/downloads/file.php?id=8665

When you create the silent voice files it automatically deletes any existing ones in that mod's folder and replaces them. It sounds like that's exactly what you want to happen, but if not (i.e., you have some non-silent ones that you don't want to replace) make sure you back them up first.

I see the big advantage of directing users to Elys' plugin is that the silent voices don't waste space. Your download is smaller, the user's disk isn't so cluttered with non-functional files etc. If you provide a voice file in a later revision of your mod, then it just stops filling the now non-existent gap.