i was wondering if the 3 lines coming off the intake pipe,(accordian pipe), not being connected would cause the car to run poorly? i know the one for the BOV can be blocked off with the use of an aftermarket BOV but what about the other two?

Yes, they are for:

1) Stock BPV
2) Idle speed control (ISC)
3) Positive Crankcase Ventilation (PCV)

so with them disconnected what would be the result?

Well, the stock BPV nipple would have to be capped, the ISC needs to be routed back into the IC piping like it is stock, and the PCV does, too, otherwise you'll end up with a bunch of problems and headaches you don't want to deal with.

so if i have been running the car like this for a while, what should i look for to fix the problems i am having? if i get new stock hoses should i be ok or am i going to have other, bigger problems?

Not exactly sure what you're asking? If you have the hoses disconnected, you need to fix them so that they're plumbed back into the system like stock.

ok, yea that is what i was wondering because i have a problem with it idleing very rough and sometimes when i put in the clutch, like coming to a stop light or something, the car will die unless i keep it running. my question was if i reconnect them (like stock) it sould solve this problem.

Yes, it should solve that problem.

ok i will give it a try and get back with you. thanks alot