So it's a 00 Civic EX
B18B/R Tranny (LS)
OBD2B - Civic Si ECU?
I think you have a bit more problems than you think.
1. CFK- you need to Bypass/jump that.
.:FFS TechNet : CKF Bypass Trick :.
2. (SP) Ignition? Elaborate on that
3. The ECU w/ VTEC does look for it's speed prior for VTEC engagement. Since you don't have VTEC. The ECU is throwing that code. This realtes to the VSS, the ecu piggy backs on the vss for vtec engament. Try to use the LS ECU. Buy yourself a jumper harness (OBD2B - OBD2A), depending what year the block is.
4. Blue Wire (Distributor) - The Tachometer is ran from the ECU and not from the Dist. on OBD2's. Therefore that blue wire is not needed although I would recommend you wire it up to the cluster, maybe that could help you out.
Hope this helps you out and gets you closer to fixing your VSS.