Did you put in an egr blockoff plate? If the egr sticks open it can cause poor idle.
Otherwise there are 2 connectors near the battery, one is just a female spade conector, this one is the fuel pump check terminal leave it alone. The one you want is a wider plug that "looks" like it should be a 2 prong plug but it really only has one prong. You need to take this connector and ground it (make sure you ground the pin and not the plastic thing inside the connector). This will tell the ecu to center the ISC motor and you can adjust the idle to ~750rpms with the biss. Make sure your logger is unplugged for this if you have one or the ecu will think your setting base timing.
You also should check the isc, I dont know if the page is still up on the vfaq but there are 2 rows of 3 pins and you want to measure the resistance between the middle pin in each row and each end pin. (ie. left pin to middle pin and middle pin to right pin). Do this for both rows of pins and it should be around 30 ohms I *think* If it is an open circut your isc is bad
Good luck, Sean.