Last year, I upgraded to Borla headers, a K&N filter, and swapped an MC2150 carb on my 258. I've noticed a HUGE improvement over stock in both performance and mpg (believe it or not!).
In retrospect, I wish I would have done them separately to determine which swaps did what. But overall, I can now hit 65mph (although a little bit sketchy...) whereas before I could only hit 54mph downhill with a tailwind.
As far as installation, I did not have to pull the motor in order to install the headers.
*'81.5 CJ7, D300, T-5, 258ci, 4" BDS lift, 33 's on 15x10 Bajas, Narrowed Waggy D44 Front, Scout D44 rear w/ARB locker, Not-so-Painless Wiring Harness, Warn 8274, Borla Headers, MC2100 carb, Shrockworks sliders, KC's, Full cage
*RIP: '88 Comanche Chief, stock except for KC lights on rollbar and custom stereo.