Subpoenas have very specific protocol. If you don't serve and prepare them correctly, they have no effect. I would not mess around with that type of discovery on your own. Hire an attorney. Really! You are also trying to prove evidentiary issues that are complicated. An attorney can advice you on how to manage your wife's illnesses or lack thereof. It may be expensive, but custody is at issue and you don't want to lose on technicalities.
Compliance with court orders are separate and apart from obtaining information as to the "why" she isn't in compliance with the court orders. If you have valid court orders, it's my opinion that your focus should be on informing the court that she is in violation of the orders instead of worrying about what potential excuses she would make for not following them.
As already mentioned, you're going to have many evidentiaty, confidentiality, and/or admissability issues to contend with if you go the route of a subpoena. I strongly suggest that you consult with an attorney to determine your legal options before trying to continue the route you're going.
Are either of you represented by counsel? Your best bet is to just proceed with the case. Do the discovery, get the pendent lite orders in place and then request trial date to get things done. The burden is on her to provide the responses and documents and to show up. If she doesn't that is her problem. If you don't have an attorney, get one.