Your Southwest 11am arrival at Midway (MDW) should work fine. Three months from now puts you in November, which is a month with a low likelihood of air travel delays. The public transit options from MDW to Union Station are not straight forward (particularly with luggage), so using a cab is a decent option. The cab should run you about $40, plus tip, and is well worth the price for door-to-door travel to the station. If you are traveling solo, you could use the Airport Express van to Union Station for $24, but for two or more, the cab is the better deal.
The first meal on the Empire Builder is dinner, so you will have to grab lunch somewhere. If you are on-time, you could cab directly to Union Station, check-in and drop your bags at the Metropolitan Lounge, and then grab something at the station or nearby. Another option is to get lunch at the MDW food court (it's a good one), then head to the station after lunch. I like eating either a light lunch or an early lunch so I feel more like dinner when the time comes on the train. The Metropolitan Lounge is pretty bare bones as travel lounges go, so (in my opinion) there is no great incentive to spend a lot of time there. When I was last there in July, I think I might have spent 10 minutes in the lounge. I showed up as the Empire Builder tickets were being collected.
The Empire Builder, as it leaves Chicago, is a huge train - at least 11 and sometimes 12 cars long. Your sleeper will be the 11th car of the train, either second from the rear (if there is a coach for Minneapolis), or the last car (if there is no MSP coach). The location of the Portland Sleeper has it's downside. You are far removed from the dining car (five cars between you and the diner) and, if there is a coach for MSP behind your sleeper, there is a lot of hallway traffic. Items like the bottled water tend to disappear from the Portland sleeper when the Minneapolis coach passengers are walking through. If there is a MSP coach, it will be removed at MSP (makes sense), so from that point westward, your sleeper will be the last car of the train with very little foot traffic. For railfan types, being the last car also means the window in the door at the back of car looks out on the track - a great opportunity for rail photos and videos.
As mentioned, you will get "free" meals in the diner, but be prepared to pay a little anyway. If you want an alcoholic beverage, that is extra. Also, it is customary to tip the dining car server, with the tip roughly based on what you would tip in a restaurant for the menu cost of your meal. I suggest that you prepare yourself with a nice quantity of one dollar, five dollar, and ten dollar bills for your trip. You will need tips for four dining car meals, plus something for your car attendant ($20 if the service is good, $10 if nothing great, zero if he or she was missing in action). If you use Red Cap luggage service at either end, you have those tips as well. Also, I like having a variety of bills to pay what is needed for the cabs at each end, including tips, without having to get change from the driver. That is just me.
This brings me to the one negative aspect of the Empire Builder to Portland. The westbound train splits at Spokane, and with that split, the dining car heads to Seattle, and the lounge car heads to Portland. Breakfast that last morning for the sleeping car passengers heading to Portland is a pre-packaged meal handed out in the lounge. The meal itself is mediocre at best (in my opinion, is was lousy, but I'll be kind). It had about six small cubes of some fruit, a very small container of yogurt, and a ham and cheese on croissant sandwich. It is exactly like a typical BOB airline meal, which is not a compliment. If you want coffee or juice with your "breakfast", you either have to get that in your sleeper (three cars back), or you have to pay for the beverages in the lounge. If you take one look at the box meal and would rather just have a danish or a bagel instead, you pay. So, for sleeping car passengers heading to Portland, the last meal of the trip is a pretty sad way to end the Empire Builder dining experience.
Having said all that, the primary draw is not the food or the lounge or the stations, it is the trip itself. You will see lots of towns along the northern tier of the country that you would likely never see otherwise. Hop off when you get the chance just to say you stepped foot in Williston ND or Wolf Point MT. The route of the Builder roughly follows US 2 from North Dakota to Spokane, so you are not even next to an Interstate. From the plains to the prairie to the mountains to the Columbia River Gorge, it is a fun way to spend two days.