Ok, the 3" body lift will prob require dealing with the fuel filler hose and transfer case linkage as well as the radiator fan shroud and possibly motor mounts.
The suspension lift will require dealing with driveline angles and a sye/ driveshaft in a non rubicon or a driveshaft with a rubicon.
With the 33's in a rubicon or non rubi you will not have to address anything else aside from gears depending on your transmission and current gear ratio. With 35's you will have to look at steering components and gears on a rubicon. In a non rubi you will have to look at axle shafts and depending on whether or not you have a Dana 44 or a Dana 35 in the back you will have to look axle upgrades or full swaps. Additionally of you don have 4 wheel disc brakes you will have to look a brake upgrades.
Alright. You have an s model. Your axles are going to be a Dana 30 up front and a 35c in the back. The 35c will be ok with up to a 33 but you have to go easy on it if you take it off road.
With 33's on a 4cyl you will likely have problems with power in 5th gear above 65 mph. You will currently have 4.10 gears in the axles and would need to bump up to 4.88's. I rolled on the 4.10's and dealt with the loss of power myself because of the cost associated with a regear.
With a 4" suspension lift on an 03 manual you should only need to worry about replacing the rear driveshaft with a double cardan drive shaft and a slip yoke eliminator (the combo runs about 500 bucks).
Bottom line is add 500 for the sye/ds on the lift and it will get you by.