Im playing with a custom intake setup 3.5 inch. I didnt really want to run the air pump hose or the front breather hose. What do you think wud be the best cleanest way to tuck these away

 

Remove from from the vehicle all together. If you don't have a stand alone to clear the cell, buy the air pump delete kit. You just upgraded your intake and shaved off what... 6lbs? Win/win.

 

I think the kit from izze racing cost about $65 shipped. It is easy to install and there are plenty of helpful threads if you have questions. this will also allow you to remove the air control valve which will not have any mounting location on your new intake ( unless of course you fab one which would be a ton of work I feel) and without a mount it will dangle onto your belt and pulleys. Izze ftw

 

where would i run the lines for these fittings... [media]https://i.ytimg.com/vi/1BN6zdjb3OE/maxresdefault.jpg[/media] (not my car) i understand the air pump hose but the front breather and the two smaller lines...

 

The front breather should be attached to the intake pipe or maybe catch can if you rather get one of those.
The other crap can be removed, check this thread out for some pictures and instructions https://www.s2ki.com/s2000/topic/112...ump-delete-kit
Keep in mind the resistor thing does not work on your US cars though.

 

is just a little breather filter a no no?

 

Lots of people run like that, you will probably have an oily mist coming out from the filter though.

 

I have just a little filter it was like $2 on ebay. It works fine and adds a little bling if you are into that. You will also want to get rid of your "hard lines" that the original breather goes through. Without the air pump or breather the only thing left is one coolant line the I.D. needs to be 1/4" and just any old coolant line will work. I went to autozone and asked for 1/4" I.D. coolant line cost me $1.70 for 2 feet (you only need like 1 foot but better safe than sorry). there are two smaller hoses that go to the air control valve I mentioned earlier. without the air pump you can just bend the rubber hose on one of them back into the other. hope this information is understandable and helps you out