I ran 30" tires on stock suspension with no rub.
What do you mean by flex fan?
Some of the electric fan setups I've seen for the Cherokee can be very hard to work with unless they are set to come on exactly right. You also don't gain very much performance-wise over the stock setup, not to mention they are expensive for a good one. I'd say put your money towards making sure the stock cooling system is in good working order, maybe with a beefier radiator, and you will be fine. I have a CSF 3 row radiator with stock everything else in the system and the highest my temp gets is 206* on a long hill climb during the summer.
I wouldn't worry so much about the oil mods. Use a good oil and filter and you will be good to go. The 4.0L has a large 6 quart sump. Increasing the capacity can actually be bad for the engine in winter, especially if you take short trips. Reason being the oil might not get up to temp and burn off the condensation. Not to mention the greater probability of leaks, which we know the 4.0 has enough of already.
If you were doing extended oil drains with synthetic in a large diesel engine like a Ford 7.3, then I'd consider a bypass filter system, but with the 4.0 you are just wasting money. The engine will outlast the body with just regular maintenance.
For performance mods the following I have noticed a difference with:
1. 63mm bored throttle body - better off the line throttle response, I recommend buying it from StrokedJeep.com, Jeff does great machine work.
2. Cold air intake with a good heat shield - better off the line throttle response
3. Dynomax cat-back exhaust - gained a solid 1 mpg and better mid-range throttle response
Other than that I would just keep your tune up parts in good condition, such as plugs, wires, etc.