I want to do a motor swap in my 99 wrangler it has a 2.5 and i want  to put a 4.0 in it what all parts do i need to do this and how long will it take  

For the time, money, and work, I think you would be better off in the long run to just get a TBI chevy V8

Find a wrecked jeep, you will need at the very least the motor and computer, depending on what tranny, the bellhousing may not match.