The engine block in the Ford GT is not the same production block as the 4.6Cobra engine. There are no parts that are interchangable. The 5.4 GT engine was all new from the ground up. Just like the 5.0 Cammer shares almost nothing with the standard 4V engine.
You can certainly buy one of these engines for your car and the earlier issues with the production engine aren't a concern.
The issue I believe is with everything driven off the noce of the crank and the 4 piece thrust bearing/washer, at high revs or high stress it's pulling up and forward on the crank causing the engine block to deform a little. Mind you it only takes .020"-.050" of distortion to wreak havac with the internals.
The facts that I stated are no big secret. For years friends of mine worked at Bondurants and I used to hear and see all the Cobra engines that they had to replace on a very regular basis. Even now, I was involved with a Miller Cup road race mustang with the current production 3 valve engine. It is a sealed engine series. Every weekend Ford engineers were going around and measuring the end play of the cranks. There were a few guys that went through 3 or 4 engines for the 8 race series. Pretty much everyone did replace an engine at some point, mostly because the engineers started saying there was to much end play in cranks. That kinda tells me it's still an issue.
I see many guys trailering home from the track with blown 4V engines. Even though the thrust bearing issues are bad the stock oiling issues are much worse.