I'd leave the shortest to avoid stress on the leaf spring at the plate. After that, choice is up to you. The shorter ones tend to be most stiff... However, too short and I suspect it won't make much difference. You'll want to keep the longer leaves because they'll yield a softer ride.
I looked at my 77' fj40 with a 2.5" lift and noticed the front shackles are shorter than the rears. The rears are a 3 or so inch conifer shackle and the fronts are 1" to 1.5" shorter. Keep in mind it has the front shackles reversed and that may have provided a little lift with the new spring mounts.
I have no idea how Iron man can sell these as a lift kit - they are too short, uncomfortable and probably dangerous, check out my thread below (in my case ironman actually agreed they were no good and took em back)
After reading Hellebore's write up on his ironman lift I am pretty sure I'll remove it and try something else, HOWEVER, I'm going to experiment first with removing the first two short leafs, and see what happens. If they let the suspension flatten out and achieve better shackle angles then great. Does anyone have any reason why I should NOT remove the first two leafs???