Essentially you'll have to trap all windows messages to the application monitor it's hadnles known windows and anything else it is exposing to the outside world and probably capture the entire screen and interpret it. Didn't say you couldn't do it, just that it's an absolute bucket load of work for minimal reward and probably poor at that.
Even then it depends on how the app was written, if it was done by a code security conscious type you could be looking at only one 'control' being exposed to windows to recieve the message queue. At that point you'd be looking at analysing screen output or simulating all possible inputs to the app so you'd know where you were.
As a for instance, how are you doing to 'know' it's running, that it has focus, how are yiou going to keep the message queue going to the tooltips come up when they should and mot linger or multiply.
Just had a fun thought could you run the app as ole or some such, then it would be in a window you control, still a damn big hairy furball though.
PS I'd be looking at C++ or some other language with real muscle to do something like this.