This is for the OP if she is still reading as some of her questions have not been answered.
1. Strollers - No strollers are allowed on the train at all.
2. Children - I was on it one week ago today and there were several children on the train. All seemed to be just fine. The youngest was about 10 months old and she was sitting right behind me. She fussed once and after that few seconds she was fine. Her parents had some things snacks for her and she was fine. There was a toddler across the aisle from us w/ parents and grandparents and between the 4 of them they kept him occupied and he never fussed once. I would not hesitate to take my kids to the top of Pikes Peak on the cog train. Take some snacks and juice or water for them and yourself (especially the water as it helps to get acclimated w/ the altitude).
3. Take the morning trains. If your kids are early risers then book your reservation for the earliest you think that all would be awake, full tummies and ready to go. Don't go in the afternoon w/ the kids not only because it might be too close to nap time but you run the risk of getting stuck in a bad lightening storm. After you go on the train and get back down it is time for lunch (go to the Dutch Kitchen in Manitou Springs for their GREAT sandwiches and awesome homemade pies

- it ain't your average sandwich place

).
4. Make sure you ALL go to the bathroom at the bottom before the train departs. They are pretty good at reminding you to go as you will pass many, "babbling brooks, tinkling streams, etc" and there is no bathroom on the train. For the younger one if your potty training or think he might not be able to hold it that long then use "bye bye pants" (aka pull-ups) for the train ride. Once you get to the top don't rush to use the restroon in the gift shop the second you get off the train. Everyone else is and you will waste precious time at the top in line. Wait till about half way between your time at the top and you can walk right into the bathroom with no wait at all. There is a changing station in the ladies room

. Oh, they might be out of toilet paper though so have some tissue w/ you just in case (this was the case last week when I was there). Buy a couple of donuts up there as well to snack on while coming back down on the train. Wait till the last 10 minutes of your to time to get back on the train and you can walk right into the food service area and not have to wait at all. Don't get too many though as you want to save room for an AWESOME sandwich and pie for lunch
5. You don't have to buy the souviners at the top as their is a gift shop at the bottom. Not as big as the one at the top but still sufficient.
6. Buy the kids a camera for them to take their own pictures. This will keep them occupied as well and make it fun for them as well. There are really cheap cameras for kids now or just buy a disposable camera for them to use on the trip. I'd get them each one so you won't have to worry about them fussing over who's turn it is. Then they can make their own memory book once they get home.
7. Whoever said that they would not do it as if you have seen one mountain you have seen them all............. oh my. SO NOT SO!!!! And would not do it with kids at all........ NO WAY!! Give the kids some memories as this is what it is all about. These things are for kids and the kid in all of us. There is SOOOOOO much to explore and see up in that area. You would regret not taking them and going yourself. The beauty of it all is amazing.
8. Make your reservations as early as possible. They DO get sold out.
On another note: Other things to do with kids while there (and I speak w/ experience as I grew up going there as a kid every summer and I just returned from the area

).
1. The North Pole - go online to their site and print off a coupon. This is only a 2-4 hour adventure depending on how much time you allow them here and how many times you let them do each ride. Go on the Candy Cane slide yourself - IT ROCKS! Always has even when I was a kid and even now as an adult. The ferris wheel might be a little too much for some kids but others are fine with it. My 10 year old didn't like it but there were tons of toddlers that were loving it. You can pack a cooler w/ lunch in it and eat there or just do the rides, see Santa, take some great pics for your Christmas cards and go eat luch somewhere else. You can take strollers here.
2. Seven Falls - again, go online to their site and print off a coupon. The younger kids might not make it all the way up to the top of the stairs (all 224 of them) but it is something to see. There is a platform across from the falls that you can take an elevator up to and get some great shots from. Again, go earlier in the day and not the late afternoon as the chance of the bad rainstorms increases then. You can use a stroller until you get to the steps.
3. Garden of the Gods, free. There are hiking trails all over the place here. Make sure you see Balancing Rock and get a photo op there. A lot of people stand under it and pretend they are holding it up. Make sure the kids wear tennis shoes or some other closed toed shoe like the Teva's, Keen's or something if they prefer a sandal type shoe. Again, this is a first half of the day spot because of the chance of rain and lightening.
It is very possible to do 2 of these in the first part of the day before any rain storms come thru or brew up. We did Pikes Peak and Garden of the Gods in the same day then the next day did the North Pole and Seven Falls.
There is also Cave of the Winds (done it before but skipped it this trip).
If you have any other questions feel free to ask or pm me. I can also HIGHLY recommend a place to stay and one to avoid. We had to experience the bad before we found a MUCH better place to stay. I HIGHLY recommend Bristlecone Lodge in Woodland Park

. (formerly known as Town & Country). Very nice and brand new cabins that will sleep 4 and a free breakfast in the morning. I also like being up in Woodland Park and in the mountains more than down in the city. Your not that far from anything either if you stay up there.