1) You'll need an automatic ECU. I belive an auto ECU will run a 5 speed car, but not the other way around. I think the fuel cutoff on the GsR is higher than that, and providing you're not revving to eight grand every single day 4 or 5 times, it should be ok if you do it once in a while.
2) You wont need a new header, the Ls one will work. If you do get a new header, get one for a GsR, Type R, or Ls as they all have taller deck heights and a header for a B16 may have some interferience issues. It may fit, and if you have an extra b16 one you might as well see.
3) You can use a VTEC harness, but it wont take much modification to change your harness. I believe there are 3 or 4 extra wires you have to run. there are not too many.