YTO is the code for Toronto - all airports as opposed to YYZ which is specifically for Pearson International Airport. This shouldn't be a problem. Kind of like on some sites you can use the code NYC to indicate all New York Airports instead of needing to specify JFK, LGA, etc.

Problem # 2 is going to be that Swissair, which the code for is LX by the way, does not fly from YYZ. In Canada, they only fly to YUL. So on the return, you'd have to either fly through YUL if connecting in Canada (not sure if AC does HAV-YUL), add an extra connection YYZ - YUL, or do YYZ-ZRH on AC metal, which can probably be booked through LX as an LX codeshare.

On the outbound, sounds like the timing issues are with the connection in FRA, not in YYZ, since it will bring up options starting in FRA.

Do you have specific flights you want to get on? If so, why not post the specific itin (including flight #s/times) you are looking to book and we can probably be a better help.

Also, have you tried using an OTA or aggregator to see if they can bring up the itin you are looking for - perhaps kayak or Hipmunk and specifying airlines (or for Kayak, *A) can bring this up, assuming the connection times are legal.