I agree about making wider time windows. Also to prevent last 5min attack it could be changed to next way:
E.g. capturing time is 18-21 in Den and Modoc.
GangA controlling Den at previous day. If GangB attacks, then they capture town in 20 min. If GangC try to recapture, limit will be reset back to 20 min. If GangA, who have city before recapture it, cooldown will be reset to 0min. But if some gang (B/C/etc, except A) managed to capture town, then no capturing is allowed until next day.
This will lead to situation, when it will be impossible to control all towns by one gang. Bigger gangs could try to capture several cities, but it will be hard for them to protect all next day.
Also town could be attacked any time (so defending, will be bored most of time). If 2 big gangs fight for one city, 2 smaller could try to fight for another.
20 minutes is good time, allow 2-3 full attacks by one faction. If time is reduced, then capturing will be much easier by big alliances.
NPC during TC
I completely disagree that they should be removed, or reputation changes disabled. Start thinking: you are trying to get control of town, and killing citizens. No town will join to you then, because if you kill npc, they start to hate you. And if faction have good reputation in town (tries to play carefully), then it should be easier for them to control, as NPC will not disturb you.