While I don't have an issue with giving a time limit to finish games, it is contingent on providing enough time for the players to position themselves for the end-game and making sure every player knows the deadline directly via PM or post in game chat. It appears that neither of those actions took place here as well as the deadline coming too quickly. If you're going to impose a deadline to finish the active games in a round, those games need to actually be holding up the tournament, not just keeping the tournament from moving quickly. You issued your 1 week warning when the games were barely 2 weeks old, which is WAY too quickly to force the issue. In contrast, I gave players a two week warning in one tournament where the games had already been played for well over 2 months. And arbitrarily deciding that only 2/3 of the players get to play their games to full length is not fair to players simply because they're paired with others who play slowly or are in different time zones.
As such, you need to allow the Round 1 games to play out to their conclusion at this point. If you still have the same games active in about 6-8 weeks, you can then consider instituting a time limit for them to finish. Also, you'll want to consider simply splitting points among players who are remaining in the games, especially if they're foggy games. A simple territory count is not always an accurate way to assess who is winning a foggy game.
Head Tournament Director