Kevin,
When I arrived in Skagway to look after the new 140 class locos, I too realised a couple of long held goals. One being that Alaska was the only state I had not yet visited. The other was to ride the WP rails.
If you are riding a Summit train, try to get on the one that is turned on the loop at Fraiser. The cost is the same but the journey is far more rewarding with some spectacular tundra scenary. Which train it is I cannot tell you and it may not happen every day. You'll have to ask.
Personally, if you cannot ride the steam excursion which is spectacular on these 4% grades, I'd ride the carcross train if you can swing it.
It is one way (return by motor coach) but with one 90 class, a box car and 3-4 passenger cars a layover at Bennett Lake with lunch it is real mountain railroading on the WP&Y.
TH