First thing first: Visa/invites (LOI).
I'm not familiar with the way RS Tours operate, but I would assume they "take care" of your visas for the tour. If they apply on your behalf for a 3-year multiple entry visa (as they should), you shouldn't be worried about adding any dates towards the end of the trip, as the visa is valid for up to 6 months per entry.
Trains: it is 90 days, period. Anyone claiming they can do it sooner is most likely an enterprising reseller (or, in a less politically correct lingo, a despicable scalper) that will take your money and sit on it until 90 days sale period opens, and then buy those same tickets on rzd site.
Over the years, I have pretty much switched to Sapsan, and generally prefer it over overnight trains. Not sure about CPAP (or wall outlets), but Red Arrow (001a) is not your only option as far as night trains go - maybe also look into Grand Express (53).
Single-sex vs co-ed cabins shouldn't be an issue for you if you book together.
Night trains of higher classes usually come with prepackaged lunch boxes, but there will also be a restaurant car.
Air museum (Monino) is awesome - but don't expect Smithsonian Udvar-Hazy kind of sterile experience. Will likely take a full day (you could still do circus or theater in the evening). Here's a community of volunteers working on maintaining and restoring some of Monino's unique exhibits - the photos should give you a pretty good idea of what to expect: https://m.vk.com/aviarestorermonino
As an option if pressed for time, check out the Central Museum of Armed Forces (Dostoevskaya metro) - they have some cold war-era aircraft outside (and debris of Gary Power's U2 inside). Closed Mo, Tu.
If you are really into air&space stuff, maybe consider a day trip/excursion to Star City (actually, more of a Star Village, Zvezdny Gorodok) - an operational cosmonaut training facitlity. Excursion must be booked 2 months in advance.
No need for guide for the Kremlin (a guide book would suffice), better to have one for the Armory (or get an audio guide). Also check out izi.travel app for free geo-located audio guides (might NOT work inside the Kremlin due to GPS spoofing). For the boat, you have a choice of older Soviet ones (cheaper, more fun people-watching), and more modern Radisson Flotilla (more comfortable, better chance of having info in English). Either way, it's more of a scenic boat ride than a tour.
As to Bunker42 - only a small portion of the original facility is accessible (the staircase, a short corridor, two larger halls, and a long corridor). If you could just walk through it, it would only take about 10 minutes. So taking the steps down (and especially up) is not only to add to the experience, but also to stretch the excursion to the advertised length of 1.5hrs.