I don't have a VRV anymore so can't take a pic of it. You have to make sure the pin is rotating the VRV like in my pic. If it don't rotate the VRV the tranny won't shift right. Look in the VRV side that faces the IP, you'll see two knobs/tabs in there, the pin must be like the pic shows.
Get yourself a vacuum gauge and do the setup like in the diagram I posted. A C6 shifts on vacuum controlled by the VRV. Put the green VRV back on if that was the original. Could be that the Modulator is ***** being it ran that hot. You can't just stick the VRV on there and expect it to operate correctly.
PM trackspeeder, he would know what VRV color should be used on a diesel. A GM VRV is different than a Ford VRV.
EDIT. Check the setting on the intermediate band, it is used for 2nd gear. The diagram shows how to set it. Back off the adjusting screw exactly 1-1/2 turns.