I'm not sure how much DOHC ZC transmissions are running right now, but Hmotorsonline was charging $200 for a non-LSD DOHC ZC transmission.
Sourcing a intermediate shaft is a little difficult(it's possible to modify the Civic 4wd one to fit IIRC); but if he has it; it's not hard at all to install. The holes are already there and you just have to tap them.
I've seen the shafts sell anywhere from $50 to $150. As for the joint, it's basically an inner joint from a 90-93 Integra; I can't say how much it'll cost because most people usually just do it themselves.
Hush22 performance has been working on a adapter kit to install DOHC ZC intermediate shaft on blocks that do not have the holes(mainly D15s and 96-00 D16s); it may be possible to build something similar or see if they offer a kit that would work with a D16A1 or Civic 4WD intermediate shaft.