Apologies for the slow response, it's the holiday over here. To your questions:
i. There's no more timer because you can stop these at any time you wish. Before there were arbitrary caps on how long you could do it, so people would just run it, then run it again, then run it again, which was frustrating. Now you just run it until you need to do something else or have achieved the desired effect, and then you stop. The functionality is identical to before (you could always stop at any time), except that it no longer MAKES you stop periodically.
ii. Well, you have the Evucks, and they have a number of nasty political deals that you can inflict on the Skylaxians to harm them. The problem with that is you want them to later be friends, of course. If you want to slow ship production, then harming the Skylaxian economic RCI is a good idea. If you want to slow population growth, then medical or public order might work (might cause disease or unrest/wars, both of which would reduce population). It's tough though, because if there are a ton of planets like that, and the Evucks are too weak to attack any of them... well, you might find you take one step forward (reducing one planet some) and two step backwards (other planets get that much stronger). It's hard to say, and experimenting around is probably your best bet.
iii. If it becomes literally impossible to win, then yes, the game is over, as Eternaly_Lost notes. If everyone was in a non-federation alliance, or if there's only one race left and it is non-federation, etc. If everyone dies, which would be unlikely but could happen.
One trick, though, is recognizing when you are beaten even if it hasn't happened yet. There are times in Chess where you're down to a king and a rook or something, and you're facing two bishops. You can lead those guys on a merry chase for dozens of turns, and if your opponent is inexperienced, you might even theoretically win. But against anyone competent, it's just a matter of time until they corner you and you're out. Novices playing novices are advised to play out that endgame, since one might make an error. Grandmasters in that situation probably will concede, knowing that they opponent won't and thus loss is inevitable despite the lack of actual checkmate (yet).
TLF is kind of the same way, where it detects checkmates but not when checkmate is unavoidable 30-some moves along the game. There's always of course the chance of luck or mistakes, too -- maybe the Skylaxians get a terrible disease that spreads between planets, for instance. Maybe you pull something really clever out of your hat. So it's hard to say with authority whether or not a game is truly lost, if you see what I'm getting at. You may find yourself in a "seeming-stalemate sliding steadily backwards" situation, though, and if that's the case then it's your option whether to concede or to pray for a lucky event to strike.
