Automatic to cobra?

I have a stock GT, I bought a couple gt40p heads, then I took those to work, and I put in some bigger valves (1.94, 1.64).
I was putting on the gt40(explorer) intake manifold upper and lower to match.

My GT is an automatic, and was wondering if I would end up blowin out the trans?
 
whats an AOD?

The transmission was built up a little only 20k ago, So I dont know if it will hold up, but I dont know what I should do
I still have to buy a gasket set, so it will be a week or two before I install them
and when I have the gaskets, Ill be able to match everything, and Ill port the hell out of the intake
 
ok, thanks for your help guys, and heres the next question, what about if I tak on a supercharger, but since I know I have a stock bottom end, Ill leave it at maybe 5lbs of boost at very most itll probably be 3 or 4