Just a heads up with the scout 44 front axle.. I have heard that there is some difficulties with installing the front "scout" 44 into a cj. It is doable and works but I just heard it is more involved than the rear, I think it was the passenger side spring mounting that was the issue.
To your question: well!! the price for a PROPERLY set up 4" vs a 2.5" will be more but if you go 2.5" you have the extra cost of the body lift so it may not be much more. I would go with the 4", but you will NEED a droped pitman arm, in my opinion a steering box brace is a must, t-case drop(which you could make your own), the kit should come with shims for the rear, longer shocks, extended brake lines. Once the lift is on you may see that your rear driveshaft isnt long enough, My 79 needed a rear driveshaft after a 4" install, but my brothers 86 did not. You may have to install a small body lift as well, or trim your fenders some. I have had fender flare rubbing with a 4" and 33,s. Oh one more thing, look on the side of your new tires. It should tell you the recommended rim size on it somewhere. If you use a 8" or 10" rim when it calls for a 12" you WILL rub on your front springs when you turn the wheel to full lock. I know 35x14.50,s call for a 12" not sure what 35x12.50 calls for, probably 10".