The implication of the episode 'Simon and Marcy' seems like this;
It was 996 years before.
Marcy was 7 ("You're scaring a 47 year old man and a 7 year old girl" was said in the episode)
Marcy was a thousand years old in season one.
About three years had passed from season one to season five (Finn went from 12 to 15)
so Marcy was 3 or 4 when Simon found her, meaning that at the time of Simon and Marcy they had been together for 3 or 4 years. This incident in the comic must have been even later!
And yes I agree. Simon was every bit the model father to her in those desperate times...