Dave, it's going to come down to personal preference...
I can see two main advantages of the Ford: simply it's a Ford, it's what people expect the car to have and it could be your last chance for you to build a Cobra with a 302 windsor. No idea with resale, won't know about resale difference until there are enough LS1 engined Cobra's around and for sale. In the US it would make a difference, but doubt it will here, we are just less traditional...
LS1 is great bang for buck, responds well to tweaking, matched with a T56 and you have a sweet combo for a Cobra. They just ooze horsepower.
Lexus V8 is fantastic bang for buck. We fitted a cheap high km one to the Harrison. God knows how many km's it has done on the track now, tough as nails. LS1 engines were much more expensive and we were not as sure about reliability with LS1 when doing a lot of track work. Lexus V8 responds very well to tweaking, just sneezing near it is enough for get HP increase.
You will also still have chance to fit Ford 351 windsor as well. US Saleen Mustang engine, they still meet our emmission requirements. They also had a factory supercharged 351 as well.
And the Ford 4.6 modular has some of it's own advantages...especially the supercharged version.
There have never been more choices...