Sorry for thread dig...
I just did an engine swap, i put an s14a engine into my s13. The motor is currently running on 3 cylinders :s I think it is the same problem as the OP as i have spark on all 4 and the fuel pump is going.
The other thing i noticed is that i have 12v on both of the injector wires on all 4 injectors. This seems a bit strange that number one cylinder is running fine even though it is giving the same readings as the other three.
Anyway, did you find a solution to your problem OP? Or has anyone got any ideas why i would be getting 12v to both wires :s? I have found a few people on other forums (after googlng) with the same problem, but so far i have found no reasons/solutions.