Yes, you need to change out the the CCV system. I my 88 XJ Pioneer owner's manual it says you are to change the CCV tubes evry 50,000 miles as an EPA emissions requirement. The basic info article will explain what you need. When you go to the dealer just ask for the CCV harnesses for an 88 4.0 and the parts buy will know what you mean. I thin every XJ of the late 80s has had this problem.
Replacing the CCV harness will fix a lot of vacuum leaks. If you have the NP231 (part time) transfer case then pick up a new front axle shift motor harness, it runs around $10. The oil filter drips oil on the harness and causes it not to seal well. If you get the "part time" 4x4 light then you do not have a leak today. If you also get the "full time" light then you have the NP242 (full time) transfer case and there is no shift motor vacuum harness fro the front axle.
I recommend you catch up on the maintenace if this is a new vehicle to you. If you are missing the owner's manual you can still get one from chrysler - $6 + shipping - for $10. I purchased one in the past year, just look up techauthority on google and call the 800 number.
Once you change the CCV tubes then turn the air filter so the non oil end is where the oil use to collect then drive for a couple of weeks to confirm no more oil on the filter. You may have a little at first but if the spot has not grown in 2 weeks it is fixed. After the 2 weeks then install a new air filter.
If you continue to have problems then have the Cat coverter replaced. I would continue to have some oil in the air box. I replaced the cat because of a noisy heat shield and what a difference. It was like taking a cork out of the tail pipe. Once I replaced the cat the back pressure problem was fixed and have not had oil in the air filter since.
Also just in case you do not have the owners manual the other 50,000 mile EPS items are: Gas tank cap, distributor cap, distributor rotor, spark plug wires. The spark plugs are 30,000 mile items, go figure!
You may ask why the gas cap. I noticed on my 88 XJ I had the smell of gas around the gas filler soon after I got it a 102K miles in 1997. I figured new vent tubes, etc but decided to catch up on the maintenance. I changed out the factory gas cap and the gas smell went away. About a year ago I had the gas smell problem again, purchased a new cap and it went away!
Oil in the air filter basic info:
http://www.off-road.com/jeep/cherokee/xjtech/engine/40ltr/blowby.htm
Additional info on cleaning valve cover:
http://www.off-road.com/jeep/cherokee/98/04_apr/valvecover/cover.html