Once I have my preliminary air itinerary and if I have any concerns, I get in touch with the airline directly rather than with GCT's travel department. I also check my seat assignments with Seat Guru to make sure I have an aisle seat and not in an exit row or a bulkhead row. The last because you might be switched with a family traveling with a baby.
In 2007, I was booked on the Russia Revealed trip and our original air itinerary was changed so that we flew British Air changing in Heathrow before Terminal 5 was opened. We had barely two hours at Heathrow on the return flight if all went well, and I called BA to check if that was a legal transfer. I was assured it was and that if for some reason we missed our flight to Boston (the last one that day), the airline would put us up overnight. We had to cancel that tour because of illness, and I finally took it last August. Again changing in Heathrow, but this was Terminal 5 and there was plenty of time for the connection.
To Liz109, I'm surprised that you were told an hour was a legal transfer. Especially, at the Frankfurt airport where you might have to take a train from one terminal to another. I missed a connection to Warsaw once because the train broke down. And especially, when Frankfurt seems to have a lot of flight delays due to weather.
I'm going to Ireland in June, and my preliminary air itinerary has me flying from Boston to Dublin to Heathrow to Shannon for a trip starting in Galway. I couldn't believe it, so I googled Aer Lingus and discovered that they do fly from Boston to Shannon, but not everyday and not the day I'm going. Flights from Dublin to Shannon in June are not up yet, so that part may change. In any case, there will be a 60 miles (approximately) bus ride from Shannon to Galway. I expect to arrive very tired, but it will still be worth it.