I can finally say I have a 95% solution and I think I'm going to settle with that.
I'm going to short-story this since it took me HOURS of diag. to figure it out.
The answer is...
Step 1: Follow California98Civic's guide on page 1.
Step 2: Disconnect the white/green wire on the 4pin alternator connector
Step 3: Ground the alternator side of the white/green wire through a low ohm resistor. I used 6.6ohm.
To re-energize the alternator
Step 1: remove grounding resistor and reconnect white/green wire to harness
Step 2: reconnect black/yellow wire to factor harness
Both of these can be easily done simultaneously with a dpdt switch.
This method will reduce the alternator voltage to battery level and keep it from putting out significant amps at the lower voltage.
I did a load test with this setup and there is no audible loading of the engine from the alternator and no real current coming from the alternator to the battery.
From my testing today it appears that the ECM grounds this wire when the car is under acceleration. I'm not sure why since it can still put out A LOT of amps at this lower voltage when load tested. The trick is disconnecting the power wire to the regulator at the same time, the Page 1 instructions California98Civic walks you through. The alternator is in what appears to be a "standby mode" for lack of a better word. The alternator is still communicating to the ECM but the ECM can't communicate back. You're giving the alternator a false signal. I'm not sure if this alone has a negative effect since I don't have the instrumentation to test it, a ScanGauge. The voltage appears to be very stable under this condition.
I don't know if this effects the alternator negatively over any length of time.
****Try mod at your own risk.****
Description for videos
Scope Traces
Yellow: Voltage regulator power, blk/yel wire.
Green: Battery light, whi/blu wire.
Red: ECM control, whi/gre wire.
Blue: Alt signal, whi/red wire.
Alternator signals while operating normally with 70amp load.
Video
Alternator signals while accelerating from a stop. Notice the RED trace.
Video
Alternator with whi/gre wire resistored to ground. (just as Honda does in acceleration video) Listen for the engine load down when a 70 amp draw is put on the battery. You can see charging amps on meter to the right. AmpMeter scale is 000.0amps.
Video
Same test as above and with blk/yel wire on alt disconnected. 70amp draw on battery. No audible loading of the engine, no significant measured load on the ampmeter.
Video
Tomorrow I'm going to wire this up in a driveable way. I'm going to be using a petal switched circuit that has a build in hold delay (prevents rapid on/off of circuit). I'll upload the schematic tomorrow for those that are interested in this method of control. It cost me about $15 worth of parts from radioshack.
insignificant note
I also wanted to mention why I did not test the alternator with the output wire (the big wire) disconnected as mentioned in previous posts. I thought it would not be best for the alternator to disconnect this wire. As most of you probably know when not connected to a battery alternators make very crude 14vdc. The battery dampens the spikes so you get smooth 14v. Without the battery on the circuit the alternator would have been powering itself (the regulator) with this rough power. I did not think it was a reliable long-term solution.