"Business Class" (not First Class) on the Cascades from Seattle to Vancouver features wider seats with more legroom, priority boarding, and a coupon good for a certain amount (I think it's $3 or $4, but can't remember for sure) off any food purchase in the dining car or bistro (cafe) car. Breakfast will be served in the dining car on your train.
I couldn't tell you where I'd recommend staying other than to find a hotel close by, even though you probably wouldn't get your money's worth out of it.
As for transferring from VAC to YVR, you could wait about 2.5 years and ride the Canada Line subway from downtown to the airport.
If your flight leaves in less than 2.5 years, your trip will require two transfers if you use public transportation, and only the short first segment would be by rail.
You could board a Waterfront-bound SkyTrain right in front of the station at the Main Street-Science World stop. If you're traveling on a weekday during daytime hours, you'll need to buy a two-zone ticket. If on a weekend, zone fares are eliminated, so it doesn't matter. The ticket you buy at the SkyTrain station will also be valid on all of the buses you'll need, provided you make the connections within 90 minutes.
Ride the SkyTrain to either Burrard (2nd last stop) or Waterfront (last stop), head upstairs (because downtown, the "SkyTrain" is underground) and out to the front of the station and look for the 98 B-Line bus stop (there may be several bus stops in front of each station, particularly Burrard, so it's important to find the correct one; the 98 runs on a one-way loop through downtown, so you won't accidentally get on a bus going in the wrong direction). Ride that route to "Airport Station" and from there, transfer to a route 424 Airport bus over to the terminal.
If you have lots of time, and want a more scenic ride (and longer rail portion), you could ride the SkyTrain the other way and get off at 22nd Street Station, and transfer to a 100 heading to Airport Station. However, the 100 runs much less frequently than the 98 does (the SkyTrain, on the other hand, runs about every 3 minutes), and you run the possible (not very likely, but still possible) risk of your farecard running out before your last segment. On the other hand, many route 100 trips are interlined (through-routed) with the 424 at Airport Station, so you could possibly stay on your bus and go all the way through.
There are also privately-run "Airporter" buses from downtown to the airport, but I've never used them and are not familiar with them. There's also the completely uninteresting "taxicab" way of getting to the airport.
Transit route, schedule, and fare info can be found
here.
