Your lawyer will of course have answered many of your questions. But divorce laws vary by state and some things you may not think to ask about.
The only custody aspect would be your shared guardianship of your older child. Expect the unexpected, most likely allegations of DV (her*) or abuse and/or neglect (children). Yor documentation can include patterns (over extended time) or incidents (specific claims). Most courts generally limit specific allegations to the six months prior to separation or filing, anything older being considered moot or legally stale, otherwise you would be expected to have separated or filed sooner.
* Courts view parental adult behavior as somewhat unrelated to parenting ability. (Almost as though a person can be two people?) So if your stbEx implies DV or makes such adult relationship allegations, that does not automatically impact you as a parent. Theoretically.
If your son lives in the house then likely she will of course try to continue living there, claiming she is the "Mother" despite her past history of not being involved as much as you in his care.
In nearly all divorces the children move back and forth between each parent's home. Can he do that? Or could he reside in his own semi-independent residence nearby? I suspect a Guardian ad Litem (GAL) will be assigned to your son. Be sure your attorney knows that not just any professional will be able to handle such a potentially protracted and high conflict case. Is your adult daughter trustworthy enough - not influenced by her mother - to relate the facts of her brothers care, etc?
The smear campaign has honestly been one of the hardest parts. I knew it was coming. I knew she’d be building her narrative with her family and our mutual friends. I pretty much understood that there was a long list of people I would likely never see or talk to again...
What I do mind: she then starts telling a woman who is literally sitting right next to me that I asked for a divorce and I’m still living in the house and won’t leave — and that she thinks I’m staying just to torture her...
All of it makes it super tempting to make a 'best hits' mix and blast out a stream to friends and family of audio and video and texts of my wife's behaviors over the years. Let's see what people think if they hear and see the truth. Not what I'm going to do. Just tempting.
I found it was extraordinarily difficult to come up with a good response in the moment, especially during a distortion campaign. For this one perhaps it would have been appropriate to comment in a general way, "We're not at that phase in the divorce, likely court will decide those details." Did you notice?
Whenever possible deflect the blaming elsewhere... lay the "blame" on the glacially slow system, the court or even the lawyers. After all, the lawyers get paid to be your buffer from such innuendo.
Years ago I posted this which occurred in my county:
Also, be very aware that these Custody Evaluation reports are highly confidential. Neither of you can go plastering these on the community announcement boards of the local stores or sending them to neighbors or the other's family and employers. The courts take a dim view of this, seeing it as retaliation or inflaming the situation. -- ForeverDad, 20 Dec 2008
I also recall my lawyer warning me not to photocopy and distribute any reports like {custody evaluations}. He said that many years ago one parent got a good report and then made copies and distributed them around the neighborhood. Doubtless the court came down hard on that parent. Remember, these reports are considered confidential. You may also be very limited in what details, if any, are appropriate to disclose to your minor children. -- ForeverDad, 23 Nov 2011
In my area evaluation reports are considered highly confidential. The story I heard was that many years ago one parent photocopied the eval and put a copy on every neighbor's car tucked under the windshield wipers. Naturally that got all the officials quite livid and I shudder to think what happened to that misguided soul. Whether that story was true or not, the evals are not posted as part of the docketed papers, I believe they're sealed by the court somewhere.
However, I do believe the courts and lawyers do try to keep the worst of it out of the court record. In all my court rulings and orders, I don't believe there's anything stated about my ex anything stronger than the time the court found she was "not credible" during a part of her testimony. Yes, the reports and evals may be more strongly worded but the regular records seem to be scrupulously scrubbed to appear quite neutral. -- ForeverDad, 3 Oct 2011