Trying to be a Time Lord

I'm 65,000 words into the current novel, which I think may be 80,000 words long when finished (it's difficult to judge) and I'm having a worse than usual battle with Time.
You'd think it wouldn't be hard for an author; after all, I'm in total control of the world I created - except when the characters get above themselves - and I'm telling the story in chronological order. I've printed out a calendar of the weeks I'm using, and have noted what happens on which day. Simple, huh?
Actually, no, and I think it's because of the structure of Unofficial Girl . At the start, Beth Chandler is duplicated in a flawed experiment, and alternating chapters tell the stories of Beth One and Beth Two, in third and first person narratives. This is harder to write than Remix , because just as I get on a roll, I have to switch to another character/group of characters. I also have to stop one Beth getting ahead in time when not much is happening to her, and there is lots of action in the life of the other.
I've tried novel writing software, but you have to learn how to use it to benefit, and I'm not convinced enough of its worth to expend the time. I can only admire and envy Gary Corby, who does spreadsheets to fine-tune his plotting. Darned if I could.
I'll just have to muddle on, grim and determined. I'll get there in the end. Watch this space.