So...what transfer case are you using? You said 241, but those didn't come in anything with a 5.3. If you're talking about the stock case, it's a 261, 263, or a 246 (if it has AutoTrac). All three of which are a terrible choice to put in a Jeep. You're going to need something as short as possible, not to mention the front outputs are female and the driveshaft slides in to the case. They're not meant to move much. There's also the issue with pump rub on all of those magnesium cases.
A 241 with a SYE is what I would suggest.
You can also set the electric fans up to be controlled through the PCM. Lots of people make harnesses for them. Just have to add two pins in the PCM connector and enable it in the tuning.
Last thing...put the air filter somewhere that doesn't let it suck hot air off the side of the radiator or from under the hood.
