Swapping a 4.0L throttle body for your 2.5L throttle body...
First off, I must say that a lot of research went into this little project and that even though the throttle body is attached by 4 bolts, it isn't just a "bolt on" type swap if you want to do it right. Attached to the '97 and up throttle bodies are 3 sensors; the AIS motor, the MAP sensor, and the TPS. These send crucial info to the PCM and can cause errors (and error codes) and do other bad thing such as foul and ruin costly O² sensors. Believe me, I know!

For '97 and newer 2.5L engines on TJ's & XJ's, you should use a throttle body from a '97 or newer 4.0 engine. I have heard that you can find a mid 90's High Output 4.0 that is usable, but have yet to verify this. The reason you need  '97 or newer source engine is because Jeep moved the MAP sensor from the firewall onto the throttle body itself. You cannot use an earlier throttle body without the MAP sensor mount, again believe me, I know from first hand experience! If you are doing this swap on a YJ, then any '92 through '96½ 4.0 source will work.

Why would one want to do this swap? Well, here are some real life dyno numbers taken from the 4 Bangers United board;
The base line is a 2.5L stock throttle body without a spacer (i.e. stock set-up)
1) Poweraid Helix throttle body spacer - +2 HP, 8% less airflow. Evidently, the helix bore has lips that extend beyond the intake and throttle body openeings and actually cuts down on airflow. But, the spacer does cool and extend air volume, hence the horsepower increase.
2) 4.0L throttle body only - +6 HP, 16% more airflow.
3) 4.0L throttle body and grind out the intake opening to match the throttle body opening - +13 HP, 29% more airflow.
4) 4.0L throttle body, Poweraid throttle body spacer, and grind out intake opening - +16 HP, 27% more airflow. The spacer is cutting off some airflow, but like in #1 it is cooling the air resulting in an increase in horsepower.
5) 4.0L throttle body, grinding out opening in Poweraid spacer, grinding out intake opening -  +24 HP, 39% more airflow.
After install, tested results were; at 2800 RPM, torque was up 16% and at 1800 RPM, torque was up by 14%.

As you can see, there is quite a potential for an increase in horsepower with this swap. Dollar for dollar, it is probably the best bang for the buck for us 2.5L guys! The guy went on to explain that by grinding the 2.5L Poweraid spacer, the helix walls still retained their properties but being ground down and rounded, the edges became more aerodynamic. Instead of trying to grind down my Poweraid spacer, I just bought a Hesco 62mm spacer from Quadratec. Same end result. He used a medium tungsten rasp followed by a fine fluted grinder bit, finishing up with a fine polisher. The intake is soft alumninum and the spacer is a harder grade of aluminum. Please note that  I  have not (yet) attempted to grind out the intake opening that is below the throttle body. This part take some serious commitment as there is no turning back once you start to grind. In addition, you need to pay special attention in not allowing ANY metal shavings to get sucked into your engine. My advice (and plan) is to completely remove the intake and have a machine shop enlarge the opening. But if you attempt it while still on the engine, I'd reccommend using a lot of tack cloth and a shop vac!

The tools I used for this swap were a 10mm socket, a set of security torx bits (under $12 at Checker), threadlock, and a can of intake/carb cleaner.

Before removing the 2.5L throttle body from your engine, crank over the engine and once it settles down, note the rpm's at idle. Then shut off the engine and remove the throttle body. Using a flat head screwdriver, unclip the throttle cable, the cruise control cable (if you have one), and the hand throttle cable (again, if you have one). Remove the air intake tubing (or funnel ram if you've upgraded) and unbolt the throttle body using a 10mm socket. Be careful with the gasket that is between the throttle body and the intake. Also, do not let anything to fall into the intake. If you take a  break for any reason, stuff a rag into the intake just to be sure. If anything falls into the intake and gets sucked into a cylinder, it could ruin your engine!

Here is a picture of the 4.0L throttle body and it's components...


Here is a picture of both throttle bodies side by side. Note: the diameter difference between the two throttle bodies and throttle body spacers...


Once you've attained and cleaned your 4.0L throttle body, remove the stock throttle body and place them side by side for comparrison. You will be taking the MAP sensor, TPS sensor, and AIS motor off the 2.5L throttle body and put them on the 4.0L throttle body. The donor throttle body I obtained came with all three sensors, but the plug ends were different. The TPS & MAP sensors went on without any problems. The AIS motor on the 4.0L throttle body was a bear. Two of the four torx bolts broke off. Being that they are tiny aluminum torx bolts, I think that the heat from the engine over a long period of time combined with the thread lock the factory uses, caused the bolts to sieze into the housing. Use extreme care when removing all bolts from both housings!

Here is a picture showing the two broken torx bolts I encountered...


The AIS motor has a paper gasket between it and the throttle body, use care when removing this as well since you can't buy a new gasket anywhere. If you look at the AIS motor housings from both throttle bodies, you'll notice that the idle air passage seat where the AIS needle seats into the housing, and the needle itself, are considerably smaller on the 2.5L. You must transfer the AIS motor and housing from the 2.5L to the 4.0L throttle body. If you don't, you may not be able to get your idle speed down to where it should be. This could trigger an error code in the PCM for the target idle not being reached (an error code 25). 

Here is a picture comparring the two different AIS motors & housings;


Once you've gotten all of the sensors switched over to the 4.0L throttle body, you can install it back onto the engine. Before you do, place one of the gaskets that came with the throttle body spacer (or the stock gasket if you didn't get a spacer) over the intake opening. You can clearly see how much extra material on the opening there is. By using a gasket as a template, you can draw a circle around the opening to use as a guide if you were going to grind out the opening. I found it easier to preassemble the throttle body, spacer, and gaskets using the newly supplied bolts and setting the whole assembly onto the intake than to try an allign each corner of the throttle body.  Tighten down the four bolts, reattach the throttle cable(s), and the filter intake tube and you are done. By switching all sensors, you should not encounter any error codes as the MPI fuel injection is a speed/density based system and does not see and increase in airflow like other systems that use a mass air flow sensor (i.e. Chevy LS1). Instead, it sees changes in MAP value and intake tempature (density in the intake manifold), crankshaft speed and throttle position, coolant tempature in all modes plus the O² sensor at idle and part throttle, and then using complex algorythems calculates the injector pulse to provide the correct fuel to air ratio. In other words, the computer seems to compensate for the swap with out any problems.

Once you've gotten everything back in place, crank over the engine and verify once it settles down that your idle speed is similar to what it was before the swap. Under the throttle spring, there is an allen head set screw that you can tighten or loosen to adjust the idle speed. Once your idle is set, replace the air filter tubing. In the throttle body spacer kit there will be a couple of bolt spacers the same thickness as the throttle body spacer. Those go between the engine and the stock air intake tubing to raise it the same amount as the spacer. Most spacers come with these but don't give you instructions.

That is it. Enjoy the increase in horsepower, but remember that it still is only a four banger!