I'm fairly new to Jeeps have done some tinkering with them but not much. I am looking into buying a 04-06 Rubicon for a project vehicle. It is going to be more of a mud trail and semi street vehicle. I want to go with a 6" lift probably by fabtech and maybe a 2" body lift, do I need to change out any of the drive shafts for longer ones or can I remain twith the stock ones for now. I have also been looking into stroker motors for it as well, looking for a good company that sells long block or turn key engines, I have thought about building the engine myself but would would rather beable to drop one in. I have also been looking into ari loackers but not sure what company to go with of course everyone has their own preferance and is hard to figure out what I want.

Any and all help would be much appreciated  

With  jeeps short wheel base, you really need to lengthen shaft and use CV's  with 6 inch lifts because of higher angles and install bump stops to limit compression travel on lifted suspension so that you do not jam lengthened drive shaft into Tcase. Also, rather than worrying about engine mods, focus on a new set of axle gears with lift and tires. New gears are kinda standard equipment requirement here but many skip it and blame engines for lack of power or trannies for being cheap when they fail for overload for big tires and stock gears. with 33's you want at least 4.56 and 4.88 is better. with 35 or more figure on 4.88 minimum and 5.13 better still. Do not let numbers scare you as you have OD and stock motor will do a fine job "if" you regear it.  

the stock shaft is plenty long enough on a rubicon  with a short, radius arm lift, adjusting the pinion angle and a t-case drop will eliminate most of the vibration you'll end up with, ya need a constant velocity drive shaft to make it right and avoid prematurely wearing out the t-case bearings.

so... yes you can use the stock shafts for a while, expect repairs later from vibration, not cause it's not long enough.

most lifts for a tj are radius arm, meaning there's very little pulling and pushing on the shaft. they come down with an arc and dont change the position of the yolk.
short arms lift only reach so far, so a 2.5" lift has the same amount of max downtravel as a 6" does, the shocks are the limiting factor. fabtech is very low on my list of good tj lifts..

if all ya want is 35's do yourself a favor and lift no more than 4"s bumpstops are what keeps the tires out of the fenders,

gears...

gears before engine mods, like snoman says there.. a stroker will do no good compared to gears and a stock 4.0..  
automatic od's (.69od) need 5.13's for 33-35" tires
3spd automatic (1-1)... 4.10-4.56
manual, ax15 (.79) and nv3550 (.73) need 4.56-4.88
manual nsg 6spd (.84)...... 4.56's
4cyl ax5 (.85)..... 4.88-5.13

on the body lift issue...

if ya raise the body you'll also have to raise the engine mounts to keep the fan shroud intact, if ya just hack off the bottom of the shroud you'll then have cooling problems... you definately do not need 6" of suspension lift and a 2" body lift to fit measly 35" tires. 37's will fit with room to spare.

lockers....

the rubicon comes with d44 front and rear differentials..
loaded with 4.10 gears and air lockers some even have a rear tracklok rear LSD along with the air lockers. they are extremely dependable and only need 5psi to engage em.

if your looking at a rubicon for 16-18,000 you'll have that much money in a plain jane tj by the time you match the equiptment of the stock rubicon even if ya only pay 8-10g's for it.

here's a recent thread on suspension for 33-35" tires
on a sister forum..
there's alot of info in there take the time to read it. the BS is minimal, I made sure of that.. use your fourwheeler screen name to login and post if ya have more questions..

http://forums.jpmagazine.com/70/6886354/jeep-suspension/suspension-and-recommendations/index.html  

Very very good info there Mud!