1) Roomettes can be locked from the inside but not the outside. When you are out of your room keep valuables hidden or take them with you. The sleeping car attendant knows who belongs in which room so you should have no problem with items being pilfered.
2) There is not much storage room particularly with two of you traveling together. There is, however, a luggage rack on the lower level of your car on which you can store your luggage. Checking your luggage at Chicago is of course another option.
3) Many people find late in the evening before bedtime is the best for showering. I am usually awake by 3:30 AM or so and find that to be excellent!!! I don't, however, recommend rising that early! : But late at night seems to work well with most folks. Soap is supplied, but shampoo is not. Towels are also supplied.
4) I'm not 100% sure on meal times, but I believe breakfast is from 6:30 AM to 9:30 or so. Lunch begins at 11:30 or 12 (don't remember which) and lasts until 1:30 or so (I think). Both breakfast and lunch are first come, first served. Dinner begins at 5 and lasts until 9 or so (again, don't recall precisely) and is by reservation only. Your dining car attendant will come to your room asking which time you like for dinner. One thing to keep in mind: Breakfast on the second morning, in the great state of Washington begins at 5:30 AM and ends around 7:30 AM or just after the train exits the Cascade Tunnel in the Cascades, whichever comes first.
5) No wifi. Phone coverage can be spotty in North Dakota and Eastern Montana, and non-existant for most of the journey through Glacier Park. Who wants to be on the phone then anyway?? The scenery is much more interesting than any phone conversation you might have!!!
6) Most stops last just long enough to let passengers on or off; only those detraining are allowed off. There are a few longer stops that are for crew changes, service stops, etc, and smoke/fresh air breaks, but be sure to stay trainside and don't wander off. Make sure to listen for the crew's "All aboard!" call. They can and do leave people behind. I was on the Empire Builder last month and they did leave someone behind at the smoke/fresh air break at Williston, ND. Williston is one of the shorter of the smoke/fresh air breaks; Minot is one that can be lengthy especially if the train is early or on-time. But do make sure at these breaks, again, not to wander off.
Other tips: If possible, try to get a seat in the Sightseer Lounge car for the scenic parts of the route, especially in Glacier Park. The journey through Glacier, if the train is on time, usually runs around 6:30 PM to 8:30 PM. When I'm traveling the Empire Builder, I try to get an early dinner time so that I am out of the diner for the journey through Glacier.
Best advice I can give: Enjoy and have fun! I live in Eastern Washington, south of Spokane, and never get tired of Seattle; I just returned from there last week. Again, enjoy!!