I have taken the train from Waterloo to Windsor, and it's really long, it seemed to be a commuter train and was much longer of a trip than the green coach bus from Victoria station to Windsor. Also, when the Waterloo to Windsor train comes in, it comes into the 2nd train station that Windsor has, which is much farther away from the castle. If you take the train, going from Paddington to the Windsor train station that's right near the castle is the better of the two ways.
I would really recommend the green coach bus from Victoria station, though. Also it gets you dropped off the closest to the castle.
If you get your tickets validated at the end of the tour of Windsor Castle, you can return for free. We've stayed at the Travelodge (the only way to search their availability is on www.Travelodge.co.uk they're not on booking.com or anything else) and they were basic but good.
I searched my family tree and found some Knights of the Garter in it, so we went looking for their names and coats of arms in the great hall that has the ceiling covered with them, and took photos. That made the trip more special, my daughter (27 yrs old at the time) loved the whole place, the shopping, everything.
Also it was VERY helpful to have a small binocular with me, to see the towers, distant gardens, even inside Windsor Castle, the artwork had name plates WAAAYYY up at the top that I never could have read without the ability to zoom in. I also find they're really helpful for reading distant schedule boards in train stations and airports, gave me a real advantage this last trip :)
When I volunteered at Pax Lodge (Girl Scouts' hostel in Hampstead) and we had older guests (anyone can stay there, registered scouts/guides get a discount), they REALLY appreciated the suggestion to go to the British Library's Treasure Room. It's got a zillion historically nifty things all in a large room with lots of comfy benches throughout, and a cafe' right next to it. If your Dad feels tired, that's a great place to go. The pub across the street was really great too, when I went in 2011. :)
Have fun!
-Alison