I'm back, and appreciate the help everyone gave me. I'll post my itinerary, just in case anyone else considers a similar trip.

• Day 1: Fly San Diego -Juneau on AS; visit Juneau by car
• Days 2 & 3: Ferry, Juneau - Prince Jasper. Stayed in Crest Hotel, Prince Rupert, which has an excellent restaurant overlooking the water. Dungeness crab was superb.
• Day 4: Skeena, Prince Rupert to Prince George. Stayed at brand new Four Points Prince George which is about a $10 cab ride from train station. Ramada is about 2 blocks from train station, and a walking distance option.
• Day 5: Skeena, Prince George to Jasper
• Day 5: Drive, Jasper to Calgary via Icefields Parkway, Lake Louise and Banff
• Day 6: Fly Calgary to San Diego on UA

The weather was marginal, but we had a great time regardless. It turns out that September and October are the rainy season, and we certainly had rain. We had one sunny day while on the train. We also drove thru some snow while on the Icefields Parkway. The aspens were at their peak color wise, a bright yellow.

Every area we passed thru was spectacularly beautiful, whether coming down the inland passage from Alaska, the train thru the Rockies, or our drive thru the Rockies. We booked Totem Deluxe on the Skeena, and had just 8 of us in a car that seated 68. The windows of the car arched up to the center of the ceiling, where there was about a 1 foot wide metal strip where they met. This allowed unobstructed views.

We had a strange thing happen re the Skeena. Our trip from Prince Rupert to Smithers was uneventful. We were to have a half hour break there, while the engineers switched due to the long travel day. After an hour, our conductors told us that there were no engineers available to drive the train onward. Apparently the engineers who were scheduled did not show up. The engineers who had brought us this far wanted overtime pay to take us onward, and CN refused to pay.

Eventually, everyone who was on the train, whether in Comfort Class (at 1/10 our fare) or Totem Class were squashed onto a bus to be driven to Prince George. CN has offered nothing to the Totem passengers for the downgrade. Giving this some perspective, it's like an international first class passenger being downgraded to coach.

I highly recommend this trip. Once I'd figured out the jigsaw pieces to snap together, it was quite easy to organize and to travel independently.