The factory radio have no amp as it's the more basic system with two plugs. The amp is going the correct way as I used the factory wiring connections along with replacement plugs for the ford harness. Just a plug and play thing was the idea.
The ford HU outputs about half wat the alpine does but if it still only netted half the extra power thats still 3x more then I had. Wasn't really trying to go for a big stereo just a small upgrade that could be removed with ease if I ever wanted or needed to.

From reading online the factory output is indeed the same as the aftermarket. If this is true then this should definately work.
Thanks