Remove the two remaining 3.5mm vacum lines on the Charge control valve (CCV) and two on the "Y"pipe assembly. Use some new vacum hose and create a "bridge" off the Y pipe to essentially negate these two nipples as shown in the pic below. The lines from the CCV also need to be plugged using 3.5mm vacum hose and a spare bolt. You should plug it at both ends, At the valve itself and at the LIM. Again you need not plug the nipple at the LIM if you do the full version.
Here is another image of this with the pipe out to. This is just for more clarification of the modification done to the "Y" pipe. Dont forget to plug the lines from the CCV as well. I did not get a pic of that.