A few things I have learned (owning a CJ7 for 10 years) is that the vacuum and carb systems on the CJs just plain sucked. What a nightmare. My suggestion, if you have the cash - upgrade to fuel injection. Either an add-on kit or a fuel-injected motor.
Remove your front turn indicator lamps and drill a small hole in the back at the 6 o'clock position - in each one. This will allow any water (that leaks into it during muddin' or rain) to drain and not short out your system.
The placement of your fuel filter needs to move AWAY from the exhaust manifold. One drop of gas from your line or filter will cause an engine fire.
Speaking of, remove that lame sound blanket under your hood. It's kindling for fire. Replace it with JC Whitney's sound/heat blanket or leave it nekkid.
If the vehicle was in a rollover, the windshield will either appear newer than the rest of the vehicle (fresh paint, etc) or the hood will be. Check under the rubber windshield seal for a different paint color. Check the seams where the hood and body and fenders meet. Look at the hood hinges, you can tell if they've been moved.
Fold the windshield down and look for rust. The front windshield cowl is notorious for leaking. People rarely know to seal this cowl with silicone.
Bring a magnet with you. Place the magnet on various places on the Jeep. If it falls off, there's Bondo underneath. The magnet will stick if it's just metal.
Pull up the carpet and look for rust. If you do buy it, make sure ALL of the holes have plugs in them so that water won't come up into your tub. Conversely, if your Jeep will get rained on and you don't have a top, make sure to pull those plugs (and the carpet) so it'll drain out the water and the carpet won't wildew. Also have someone stand in front of the Jeep and shine a flashlight at various spopts on the firewall. You get inside the vehicle and look for light leaks. If you see light, there will be water leakage too.
Look at all the body bushings and suspension bushings. The stock rubber could be rotten.
Look on and under the engine for oil leakage.
Try to move the upper part of the front shocks. The top half of the shock mounts can often crack the welds but since they sit in a tube-like area, you'd never know they were broken.
Check to see that all electrical things work including the wipers and all lights. Sometimes it's not just a burned out bulb.
Check to see that all heating and vent cables work and are not stripped or snapped.
Check underneath for damage to the axles, differential covers, etc.
Ask the seller if he or she has service records. You want to know if this person took care of the vehicle. If engine oil, differential oil, trans oil, transfer case oil were not serviced, you'll have big drama later on down the road. Ask how often the vehicle went off-road.
And last but not least. Jot down the vehicle's VIN number (ie 1JCCXXXXX...) and get it checked out with carfax.com. The VIN is located in three places - make SURE they match or the vehicle could have been stolen or been an illegal salvage. They are located on the firewall - a square plaque that's riveted to the fireall on the driver's side. Another location is just inside the driver's door sill on the inside - you'll see a sticker. And the main one - the one that parking meter maids look for is riveted to the wiper motor cover on the driver's side just behind the glass and in front of the padded dashboard.
Good luck and welcome to the addiction.