K&N filter install

I put in a K&N cone style air filter in my 1990 4.0 MJ.

Now I Have the PCV tube and the vacuum lines for the EGR and something else that dont have a home. Do I need to put these back into the intake or will I be fine leaving them disconnected?

put them back
make a hole in the same type of place as is used to be.

You should have a breather line coming from the valve cover (hook this to air tube), small vacuum line that controlled the flapper on the front of the airbox (plug it since you don't have the airbox anymore) and one larger line coming from the charcoal canister (run into airtube or put a PCV breather on it).

Some may argue that the charcoal canister needs to be going into the intake and they're right to the extent that this is correct for emissions control but not necessary for proper engine use. Mine has a PCV filter on the end to keep crud out (overkill) but is not presently attached to the airtube where it would be evacuated each time there is vacuum present.

With my 1990, (renix) I had three lines, one from the PCV which i drilled a holeand put back into the intake tube. Another was a vacuum line that went to "bank" of vacuum lines, I also used a bung and have that one set up into the intake tube. the other was for the EGR flapper, which I just left alone.