I stayed in highland resort at july2007 and feb2008 (as my son is a thomas fans), highly recommend.
1) July2007, i booked from internet because i want to stay in Thomas character room room502, but need about $3000 without BF/dinner.
2) feb2008, i booked from egX (normal room), about $2400 with bf+dinner.
3) both include hotspring in a beautiful building
4) both include entrance ticket to fuji-q(thomas land).
5) my trip: day1, take a bus (thomas bus at 12:10) from shinjuku, arrive at around 1:45pm (directly to the door) , check in, lunch, rest, enter thomasland without buying ticket. day2: BF, buy ticket (kid-ride pass for mum and son, normal ticket for c6), lunch at hotel, back to highland again, leave at 4:00pm to other place.