Here is a link to a page which gives some numbers for the 2.5 throttle body swap:
4.0L throttle body swap
If these figures are accurate, is seems that swapping out the throttle body is easily the biggest single improvement for the money, as bored out bodies are available on eBay right now for $90 plus a core charge. Other things, such as the electric fan conversion, air intake and exhaust modifications help too, but all cost much more, and their gains are smaller.
So, while a 4.0 still makes more total horsepower, given that the 2.5 engine weighs hundreds of pounds less than the 4.0, the difference in power to weight ratio looks to have just become quite a bit less.