Just my own $0.02... and I havn't done anything with the lincoln yet... but I put a bunch of B-Quiet products in my truck; roof, back wall, floor, doors... I did the whole thing except the firewall (didn't want to go through the PITA of pulling the dash off). Let me tell you; I've never heard such an improvement in my life. For me, I had JL components in each door as well as for the rear speakers, JL 10's, and an autotek amp (not well known and very under-rate) running all of it, with an alpine head unit. In my own opinion, the sound deadening made more of a difference in sound quality and harmonics than the stereo alone.
I don't know exactly what the lincoln has in it from the factory; given how quiet the ride is, I'd guess it's got quite a bit in the passenger compartment. If I were doing it, I'd cover the whole trunk myself and most likly leave it at that unless I started replacing components up front, then it would depend largly on what I find already there.