What Ford needs to do is offer performance upgrades (ala SRT) that don't void the warranty. If I had the option to have "approved" mods performed at the dship it would be a no brainer for me. I'd happily pay top dollar to keep my warranty intact. I'd be fine with paying a higher warranty deductible too.
The other option would be for them to form partnerships with "approved" tuners such as Livernois who they apparently work very closely with already. I'm pretty sure Livernois knows the design limits of these cars and does everything they can to make safe reliable upgrades. Ford knows this but they want to have it both ways. They want the collective knowledge the aftermarket provides (hence their participation in SEMA with dollar cars provided) and at the same time being able to screw people out of their warranties.
What Ford should take from this, the billions of dollars spent in the aftermarket is that manufacturers aren't building the cars we want, we are just settling for what we can get. Their processes are broken and outdated. Start offering more options, encourage folks to order cars the way they want them so dealerships can stop having to carry millions of dollars in inventory that Ford has to heavily discount at the end of each model year.(which in turn murders our resale value)
They could have built a SHO that trounced anything south of 100K, and to be fair they come close in many metrics but with every Ford i have owned (Which has been quite a few) I always end up with the feeling that someone decided "it's good enough". If manufacturers built what their customers wanted the aftermarket wouldn't exist.