well, it's not the dist. then.
I'd try resetting your ECU after any major mods like that(port/polish). Disconnect battery neg. cable, step on brake pedal to drain any residual power stored as capacitance/inductance, then restore power and start car. If that doesn't work, which it might not, then something may not have been hooked up right when the manifold/TB went back on. Check your sensor connections and vac line connections, especially for the MAP, IAC, TPS sensors. Honda ECUs are pretty forgiving of mechanical mods as long as all the electrical signals are present.
As for the cable tranny, I've noticed the inner cable does stretch over time(150-200k mi.). I assume you can't adjust it tight enough to get the clutch fork to move? I dunno there. If the adjusting nut's at the end of it's travel, i'd say look at how both ends of the cable are connected , make sure nothing's wierd, then start loking for a new cable.