-The one going to the FPR should be fine. That is the one which went to the stock FPR? Also you should note that if its an aftermarket FPR you dont really need to connect a vacuum line. For non turbo you dont really need the rising rate, it will just run the same pressure all the time. I dont run a line onto mine at all.
-Those 4 nipples you have looped underneath the throttle bodies is what I used for the microtech MAP sensor. I used a t-piece to connect them all together and then to the MAP sensor. It probably wasnt ideal for MAP readings, but it ran perfectly. It depends how they tune it.
-Using the ISCV is better for idle. Even if you dont plug it in, when it is turned off it will still allow some idle control without having the throttle bodies preset open. Using the adjustment screw is good for fine adjustment.
That is how my 20V was setup. With a decent tune it started first time everytime, idled around 1000rpm and ran perfectly.