Is it a JWT ECU? I believe they charge a lot less for a reprogram once you already purchase one off of them. Since you already have it that would be the cheaper route but you could also get a Nistune or Zemulator and program it yourself, but it'll cost about the same as the initial JWT tune.
I used the Z31 manifolds and modified the left manifold to re-route exhaust to the crossover pipe then put the turbo on the crossover pipe. I moved the battery to the back and that made plenty of room for a turbo. I was going to remake the exhaust manifold setup using two right manifolds from a Z31 that ran two separate pipes to the turbo for better flow but didn't get a chance to before finding the rust.
Here's my oooooollllldddd article on turbocharging the Maxima:
http://www.nicoclub.com/articles.php?id=158463
This page has some pictures and info of the setup but before I got to clean it up... the intake and exhaust design were flat out terrible at the time:
http://www.cardomain.com/ride/177457