All of those are very good questions and i can only speculate because i do not know too much about the altima qr25
What i can tell you is that the precat issues are apart of the exhaust manifold and not the engine itself. Specs and Altimas of that year have the exact same manifold, it is just the spec-v drivers drive their cars much harder and that leads to the cat break-up. Replace the manifold with an aftermarket header and problem completely solved.
As for the intake manifold i have no idea. The altimas may or may not be the same as the spec's, and i do not know if they used the altimas or the spec's when they did the swap. If id does have the butterfly screws then just lock tight them and you will be fine.
Performance wise, as long as they used the spec's computer you should get all the hp. I know that the difference between the 02-06 ser and spec-vs is all in the tuning and not internals, and i am assuming that the ser and the altima have basically the same tuning.
Hope all of this helps
