Were you able to check fuel pressure? My Honda service manual says that if you get the random misfire code with the accompanying individual cylinder codes (regardless of which cylinder or how many), to check fuel pressure.

 

Knock sensor? They're easily damaged when dropping the tranny and a fracture in the "microphone" could lead to fuel cut....

 

Interesting. How easily damaged when doing a clutch job? How likely would this be my problem. Would it cause a lopey idle as well?

 

so how many probs do you have with the car? idle surge? misfire? etc..etc..
a bad knock sensor will not cause misfire or logpey idle. when eng. detected knock , it will retard the timing.also it will throw a cel.
Lopey idle could be the cause of intake leak, IAC valve stuck. bent throttle plate etc...