not to try to knock off what anyone else has said, I agree with everyone else, but the knock sensor will NOT put a honda in safe mode. . . My brother drove on a disconnected KS for a month before he got a new one, there was no change in how the vehicle performed. Granted I totally understand that the KS retard the engine timing if it detects detonation and he shouldn't have driven the car hard, but under NORMAL driving the vehicle will not harm itself.
As a matter of fact, I don't think the KS even gets looked at by the ecm until the engine engages VTEC, I could be wrong, but I have only known the CEL to come on for KS if the enigne is revved high.
Also, I noticed that you have mugen chip listed and greddy fuel management listed, neither of which has a safe mode that I am aware of.
Tell me, does the car still bog if you put in the stock ecu???
Check the plugs that I mentioned before, I still think that your problem lies there with the bogging.
as far as the knock sensor, did you run a shielded wire to it? The wire needs to be shielded because it can ger interference from just about any other wire that it is near (also happened to me), a shielded wire has braiding around it that needs to be grounded so that no interference gets in it. (alot like spark plug wires)
check into this stuff and then let me know how it goes.