Please Help!! - 4.6L Prob.s

[98gt5sp]

I recently found that a connector rod bearing in my 98 4.6L GT was bad (causing a loud, repeating, clicking noise at higher RPMs), and therefore had to take it into the dealer. Since my car is still under warranty, they are putting in a remanufactured 99 4.6L engine (it should have a significant amount more horsepower with the stronger cylinder heads). Much to my dismay, I heard several things about the remanufactured 4.6L engines, including "It will only last you 30-40k miles," and "you will never be able to move to forced induction or take it over 350 HP naturally aspirated,". If anyone knows anything about these remanufactured newer 4.6Ls specifically, I would greatly appreciate any info. I am wondering if I am going to be okay or if I will have to buy a new cobra short block in the near future to avoid problems with this engine at higher horsepower. Thank you very much for your help,

-98gt6sp