the one that went to the dump valve must remain blocked

the other 2 that were originally to the air box must be opened up to atmosphere or put back into the inlet before compressor. you will have big problems if they are not.

the small one from the SEM valve is easy. just remove the hose completely and leave the port open at the valve itself.

the breather is normally dealt with by piping it to a catch tank of some kind - if you have removed the airbox, you can put in one that is a mirror image of the coolant header tank. most people who like things to look bling use a polished alloy one or some such crap.

bodgers have been known to just pipe it to a coke can or something, or i have even seen a plastic bag

personaly, i would have kept the air box with guide air duct and plate between intercooler and radiator and put a k&n panel filter in it