We leave June 20 out of Seward. Will take the train from Anchorage. Told we have to be at a convention center or something by 10 am on Sunday. Train leaves at 12:30 and arrives in Seward by 5:15. Boat leaves for us 8:00. Don't know if this applies for you as well. I'm looking into a glacier flight by Alpine Air while in Anchorage. Hope this helps.
If taking a bus to Seward- they leave continously from Anchorage from morning. 3 hour transfer- sit on the right for the best views. You will likely NOT have time for both a Kenai Fjords tour and glacier helicopter landing. A better and cheaper option than the cruise rail is to take the regular run of the Alaska RR leaving early morning. You'll be in Seward around 11am. And likely to catch a 11:30am Kenai Fjords boat trip- I do not recommend anything less than 6 hours on the water. The regular run of the rail road is also about $40 cheaper- you need a $5++ cab x2 if you go on the boat tour. (have the cab wait while you drop off your bags- or Kenai Fjords will store your bags). Any helicopter trip will have to be booked in advance, check the schedules as this tour is shorter than the boat tour. If you choose the cruise bus/rail it may fit your schedule better.