From your question, I suppose your first name has been changed legally already ?
In this case, I would ask your previous schools to change the name on your official degrees/certificates on the basis of your legal name change documents.
In any case I would apply by your legal name (so that the person who gets into a university legally "exists"), and without mentioning being transgender (it is not a disability/something which might affect/hinder your academic performances). I would also list your past schools on your application; chances that they will ask for official documents from these schools are - probably - very low.
In the worst case, you might have to explain the situation at a later stage of your application... in my opinion it's still better not to out yourself from the beginning. (But this is a personal opinion)
Personally, I applied to universities (in the UK) by my legal, still female name, waited until my offer was unconditional and having been officially enrolled, before revealing my transgender status - the staff at my uni were all very understanding and then changed my first name and gender on all documents/email accounts etc, and even gave me a second accomodation contract so that I could have male flatmates (instead of the female ones originally automatically assigned to me).
I think it's up to you... if your ID and recent certificates read male, I could understand wanting to be 100% "stealth"... how relevant are these 2 years at school under a previous name in terms of getting into uni or not ?
Good luck !