Don't know if this is posted somewhere already but I just swapped an intercooler engine into a nonintercooled truck. These are some of the differences I found.
-The engine fan has a different mount. The intercooler fan sits higher and a little left of where a nonintercooled fan sits.
-The intake air horn on the intercooled engine is farther forward than the nonintercooled engine and won't clear the intercooled injection lines.
-The delivery valves on the rear of the pump are longer on the nonintercooled pump.
-vacuum pump is different but interchangeable, just need to add the oil line for the intercooled pump.
-lower rad hose fitting and bracket is different. The air conditioning mount is different on the bracket and the tensioner pulley mounting location looks to be different which may not be a big deal but the factory belt may not work if you don't change it.
-thermostat housing is different. Nonintercooled housing faces forward and intercooled housing faces to the drivers side.
There are probably more difference but this is a start. Things that I noticed.

 

also none inner cooled have bigger injector's that's why alot of guy's inner cool the early truck's then they really Fly .Also core support is different so is Placement of headlight's and grill

 

Different length belt, Injection pump, Injection pump timing, Turbo housing, turbo inlet 3" vs 4", injectors 9mm vs 7mm, Chassis is taller under the cab on I/C than non, Different radiator, Non I/c used a voltage regulator just to name a few.

 

Timmy22,
The timing is different too?
Which has more timing, the I/C or the NON I/C 12V?
How are you liking the 4 BT Jeep?

 

Non I/C was 1.35mm 1.40mm spill port timing. The I/C models used 1.25mm spill port.

You take the static advance desired, divide it by 5, then add it to the lift to port closure for your total advance.