The easiest way to check all of those things would be to take the turbo off really. That way you can have a good look at all aspects of it and the maanifold and replace the gaskets at the same time. The standard manifolds are very prone to crack on the third runner and they are mega restrictive. if you remove the standrad heat shield (if it still has one) you'll see the manifold and it may be obviously cracked, but sometimes the crack an be underneath or in the collector. The wastegate on the CT9 often has one or more big cracks but that more often causes boost creep than lag but worth checking. If you do take the turbo off, check for shaft play etc. You can get a replacement CT9 reasonably cheap, i think there is one for sale on JDM EP.