Our stroller isn't a jogging stroller, but it is the 3-wheel type - Jeep Liberty stroller (the front wheel swivels). Even though the front wheel isn't fixed like on the typical jogging stroller, it was still a pain to get on and off the trams. Remember when you drive to MK you will probably need to take the tram since the parking lot is huge (and then the monorail or ferry to MK). AK has trams as well. Sometimes if you get there early enough you may get a parking spot close enough to walk to AK or the TTC but I wouldn't count on it. The front seat in the tram cars are double seats that face eachother so if you pick one of those rows you shouldn't have a problem fitting the stroller on (folded up of course). If you take the bus to MK then you are dropped off right by the main entrance, not the TTC.
I have seen people wheel joggers onto the monorail just fine so you shouldn't have a problem with that. We also took our stroller on the bus a few times. Not a big deal. They are the typical public transportation type buses. I also read recently (here) someone said if you go to the back door of the bus (which is a bit wider) the driver will let you load on there first. We never tried that so I don't know if that is true of all the bus drivers but you could try it. I actually thought the aisle on the bus was fairly wide, though.
HTH and have a great time!
Cheryl