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In Son of Dathomir, Maul is seen by the Jedi teaming up with Dooku, and Windu starts to speculate that Dooku is the second sith and Maul his apprentice. By ROTS, after Dooku's death; the Jedi Council assumes that killing Grievous will win the war. Did they totally forget about Maul? They knew he was out their somewhere. I know obviously this is because ROTS came out in 2005, and Son of Dathomir came out in 2014, but what is a good in-universe reason for this?

Darth Maul wasn't the general of most of the separatist army. With Grievous out of the picture the sepratists were all but leaderless and Maul wasn't filling in the gap

We can't tell until we find out what happens to Maul post-SOD. My guess is he pops up somewhere after RotS.

And Maul appears to be out of the picture in terms of legitimate military at this point. The crime syndicates left him and most of his Mandalorians were slaughtered. He might not be a concern for the Jedi Council at this point if he chooses to fade into obscurity.

Because stopping the War wasn't really about whose a Sith and whose not (from the Jedi perspective).

It was about destroying the leadership of the CIS. Their minds got turned to why Palpatine refuses to stop the war and why he won't give his his political powers/leadership.

That was the focus of ROTS.

Whilst Maul being an active Sith was just a theory, one Kenobi would probably tell Windu later doesn't make perfect sense. As they know Maul was revived sometime late in TCW, and Kenobi knows Maul took his own apprentice (Opress) and trying to make his own army, again very late into TCW.

I think we're reading to much into this, the reason why neither the ROTS novels and such note that Ahsoka Left the order, Maul is still alive etc, is because they were(and Before somebody says "you don't say" or "captain obvious here me out) the novels and movies came years before the TCW and SOD. It really surprises me that lucas and team gave the greenlight to make that happened, however it could be that they plan to release new novels regarding the events of ROTS sometime in the future.