1) Flags are often the way to go
2) The victory condition spawns right before the units actually spawn, so in the split second before the heroes arrive in the level. Fix this by not setting a 'win_game' there, but a 'set_timer'. Then put the victory condition separate, under the condition that timer is above 40 or something (so you win 2 seconds after you kill all units).
3) Yes, pick a different computer player. One that fits your needs.