OK, let me start by saying I have not dyno'd my Jeep, so everything I say is not backed up by data (it is from a theoretical point only).
Regarding the fan, in theory, switching from mechanical to electrical should result in some loss, so when the fan is actually on, it is less efficient than the mechanical fan when it's on. The good thing about the eFan is that (with the right controller), it will be off when it is not needed (say, when you are driving 30mph or faster). Also, the speed of the fan is independent fromt the speed of the engine, which means if you are rockcrawling in 4L, you can turn the fan on a full speed and it will cool a lot faster than the mechanical fan.
Now, to say I have noticed a drastic change when switching from mechanical to eFan would be a load of crap. Does it help? Yes. Is it a night and day difference? NO. Would I do it again? Yes. Does it free up some ponies? Yup. Will you feel them with the but-dyno? Probably not, but you will be less likely to shift down to 4th on the freeway. In my case, I did a prior run to see where I needed to downshift on an overpass in Miami, and with the eFan, I would not have to shift until higher on the ramp. Later, with the 62mm TB, I did not need to downshift at all... Of course, the test is not 100% scientific because it does not factor in the wind speed or the fuel weight (fuel tank at different fill levels), so keep that in mind.
As for the Flex-A-Lite, I have no gripe with them other than why pay $100+ when you can get something just as good for $30 (ford fan).
Now, regarding the TB, what you really want is no restrictions at all. This means as straight as possible piping from the filter to the TB with no restrictions (ie. the diameter is always constant). Now, the intake manifold can be opened to 62mm (I think even 63mm is still doable), and the 4.0L TB can be bored out to the same. TBS you can make your own or bore the one you have out to take maximum advantage. By the way, if it has that spiral thingy, that does nothing to help your HP... You want a SMOOTH surface...
As for the air pressure, I would not worry too much about that; in my opinion, the formula is simple: you need air, fuel and spark. For more power, you need more fuel. To burn more fuel, you need more air. The ECU will compensate, so more air and more fuel will give you more power at WOT only (something to keep in mind). By the way, I run a little higher pressure than most (46PSI) to compensate for the 62mm TB, cam and other doodads that I have on my rig...
As for the plugs, I have run the accel coil and the Screaming Demon ones; I have gapped my plugs at .060", and it still runs nicely, but I have also fried my coil, so I am now considering to lower the gap a bit (especially since I got a 600 mile road trip coming up; last time I made the trip, I ended up having to swap coils in the middle of nowhere at night under the rain! NOT FUN!).