Hi,
Luckily, there is ONE Alaska RR main line, Anchorage-Fairbanks.
Also, two lines south of Anchorage to Witthier, and Anchorage to Seward. Those are superb lines, scenery-wise. Not too long.You can spend 2 days doing those, then spend a full day going North to Fairbanks. ( north of there on a relatively short branch : freight only.)
Then, you can make your way back down to Anchorage on the same train, another day.
The cruise ship connection is near perfect: Cruise on a ship arriving in Seward, take the train to Anchorage. do your railfanning. Then take a cruise departing from Witthier which requires the train to the pier.( or vive-versa of course)
Witthier: Princess Cruise; Seward: Celebrity , Holland America and Regent SevenSeas.
We did that in 2004;; FANTASTIC . Took the ''cruise'' package northbound, ultimately ending up in Fairbanks. Then, did the ARR on our own, great trip !!...then took the train to the pier at Witthier and sailed back home !!
If you want a ''lesser'' cruise experience ( just about as scenic and fun ), take the Alaska Marine Highway ( vessels...) from Bellingham to Seward.
Great plan
Good luck