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Mike, if say I should be able to drive my car to your neck of the woods how much time would you need with it to figure out if you could install something to make my assist not come on so much? If I got the electronics shop manual for my HCH I would it have info in it that you would need or could use?

Tom,
The electrical and regular service manuals would be necessary. When you say "make my assist not come on so much", I don't exactly know what you mean.

Do you want to only have normal assist activation but reduced assist level?
Do you want assist to not be as agressive, and only come on when at nearly WOT?
Do you want to be able to shut assist off at your command?

The civic uses serial communications to control assist, rather than the PWM hardware control that the Insight uses. Once the communication was decoded, a MIMA system for the civic would be possible, and could be simpler than the present MIMA. The work is in the decoding of the communications. Honda does not publish any information that I have found describing that communication.
I will see if I can capture that communication when I get my hands on a HCH at the next UYV, as the first step in that process.
;)

Does it by any chance send the data over the obd II port, or is it an isolated system? Do you think an obd II controller could actually reprogram the parameters?

As far as your questions. Any of the above would be acceptable.

BTW, as a gift to you I can try to get you the manuals.

As far as I can tell it is an isolated system.
The manuals will not help much except to show on which connectors the signals are available on. To decode the signals, the serial data will have to be captured, while observing the operation of the assist and regen. The problem is that no information is published on the communications, so one must determine which of the many signals passing through the serial buss is the assist/regen control by trial and error. Serial communications usually have checksums at the end of each communication, so simply removing the assist command would set codes, as the checksum would be incorrect, so a new checksum would need to be generated with the modified command.
There may be a simpler hardware assist disable trick we could play, but without a car to tinker with, no way to know.
After spending all of the hours that I did on MIMA, and only selling 30 of them to date, I am not too keen on going down that road again.