The electrical load issue would be related to the ELD (Electric Load Detector) found in your under-hood Fuse box. I'm not sure if there is a test procedure for the ELD but you might search on
Honda-Tech as I remember there being and ELD specific tech thread in there.
ELD Thread 96-00 Civic related but may still contain useful info.
HOW TO CHECK THE ELD
ELD Search
The HF under-hood fuse box has an ELD in it as well as the VX one. My only concern would be if the wiring is the same to the pins on the ECU.
The ELD detects things like the blower fan or headlights putting more of a draw on the electrical system, it then tells the ECU to kick up the idle a tad (100-150RPM) by changing the position of the IACV.
I have personally seen the HF ELD go bad before and the symptoms were a weak idle and dying engine in idle when headlights, climate control, or radiator fans turn on.
Sometimes the idle will bog for a second as the headlights come on or the cooling fan turns on. Sometimes the system takes a second to catch up due to carbon buildup in the intake or IACV.
I find my VX "pulsating" as you've described while lightly accelerating. I believe it to be a measure of the ECU programming to save a little gas during acceleration. It may be more noticeable in your HF as it is even lighter than the stock VX.
The ignition timing will retard and advance under idle as the ECU is compensating for lean/rich mixture, this is normal.
In order to check true base ignition timing you must jump the service (CEL) connector on the OBD1 ECU and check timing that way. Since you've done an OBD0-1 swap you'll have to check to see which ECU pin to ground in order to get into diagnostic mode.
Have you cleaned the EGR passages?
EGR Cleaning How-To
Hope this helps