Why would you relocate your battery for a D16Z?!?!
Anyway, for the B16A I personally wouldn't use most D series intakes (AEM, etc) because the intake itself is actually smaller than the TB! What good is that? If you don't want to relocate your battery I think you have about 2 options.
1) A lot of people are using intakes from the 90-93 Tegs. They are for B series motors and they're bigger in diameter (I believe its 2.75") and they're bent perfectly so they should fit around your battery. I've never heard of one not fitting.
2) Injen CAI for an 88-91 CRX Si. The piping is the same size as the 99-00Si (again, I believe its 2.75") and you won't have to move your battery for this one. I don't know why, but injen just made the piping for this intake bigger than all the other companys.. Works for me.
That what I'm going to get when the time comes.. I had my old shorty that I had on my ZC when I dropped my B16 in, but it was just too damn small, so I took it off and replaced it with a stock one with a modded airbox.