Obviously your turbo guy has never built a D16A1 before.
There are no aftermarket intake manifolds available. The only options are to find a ZC intake manifold or fabricate your own.
The exhaust mainfold is a different story. Any D-series header/manifold will bolt up, but you will need to do some port matching.
No other tranny will swap or be worth the hastle of swapping, just install an LSD. The tranny is the least of your worries, it should hold up to whatever HP you can throw at it. Many people with mid to late '80s Hondas actually swap the D16A1 tranny internals into their tranny case.
24 lbs of boost?! What have you done to the motor to support this much boost? 24 lbs is insane!