I hate to do this, but if you had searched, you'd find my post from April about my smog test.
Drink me FWIW, I threw my pesky "Bank 2 Cat Eff" CEL on the way home from the test. And still passed with flying colors on the 15 MPH loaded (chassis dyno) test.
In PA, a motor of my type (hybrid) is supposed to be tested under the more stringent of the two conditions (2.5L 98 or 3.0L 01), but since they are the same here it didn't matter. I posted that later on in the thread. No way anyone knows what you did unless you tell them or they pull the heads (and realize the cylinders are much bigger than they should be).
Then Big Jim typed a big post in General about smog theory. Very interesting reading.
As far as selling, I don't see any reason why you'd have to tell the DMV about what you did. And even if you did, as long as you are smog legal there shouldn't be a problem. Disclosure to a potential buyer would be nice (I doubt "buyer beware" holds if you hide the fact that you have major mods like that, and it's probably a selling point anyway).
I personally wouldn't let a Ford dealer touch my motor because I don't have one near me that I trust that much. Many of them have trouble working on stock motors with a shop manual handy. If I can't do it myself I'd just take it back to the guy who built the motor in my case.