Wow, long time since you were on the Ford GT forum. I had both as well. Overall, I'd buy the Cobra again before I'd get another GT. My wife hated the Cobra but after I got her a car with air conditioning, regular seat belts, a power port for her ipod she didn't go anywhere with me anyway.
My car had a Roush 427IR which is Windsor based. Mine was fuel injected which you might find beneficial if you drive through altitude changes. Other choice is a FE.
Get the Tremec tranny.
There are parts supply issues plaguing a lot of the engine builders you find here so if you want an engine arrival to coincide with your chassis you should get started with your purchase post-haste.
You're correct in using search and soaking up the existing knowledge. You'll find that almost anything you can ask has already been asked and answered, and most of those multiple times.
PS. What happened to the Florida part of your old name?
PS. I didn't connect that yours is a 289 car. Good choice. I always thought the 427's were "over powered" and weren't happy on the street and begged to have the cobwebs blown out after a few miles of street driving. Sources are all still struggling with component availability so start searching now. You might also want to consider an crate engine from Ford or Roush if they have them in stock. Just don't let any GM product get near your car.
