Hey Mark,
Ok I'll try and go down your list one by one:
1) Showing a comprehensive list of tracks. To do this you can select your files and drag them into the GE window. This should automatically load the files in the left panel. By default it should select the tracks, but double check that there is a check box next to all the tracks you want to include. Also, there should be a time scale in the upper right (if not, go to the Tools or View menu to make it visible). Make sure you set the range as wide as it will go so that it includes the data for all the dates/times.
This is what I do, and then I create a KML file and I'm able to embed it into Google Maps. Like this: Atlas Rider » Maps
2) You will have to do some organizing with your GPX files. Like a folder for each country, then drag all the files into GE.
3) To fill in the gaps you can get directions from one point to the next. You can't do multiple waypoints (it sucks, but no way around it). After you get directions, in the Directions pane on the left you should see an item that represents the "track" for the directions it mapped out for you. Drag and drop that into the MyPlaces or a folder within it you use to organize your tracks, and now you can include that to fill in the gaps. Save everything together as a KMZ file for future reference.
4) Like I said in #1, take a look at how I've done it. You can embed it in Google Maps by specify the URL of the KMZ file you created. Then take Google Emed code and you're all set.
Hope this helps!
Atlas
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