I am pulling the clutch, pressure plate , throw out bearing and new pilot bearing. Is there anything else I should do while I have tranny and T case out. Keep in mind that I am wanting to put 12 inches of lift and run 34 inch tires, as the end result of my build.

I would have the flywheel turned.
I would replace the rear main crankshaft seal.

Although the following was written about the Samurai, the basic concepts should generalize to the Sidekick:

While the Samurai suspension is easily modified to add lift, it does have some limiting factors associated with it. The stock Samurai drivetrain is limited to 6” of suspension lift (+/_ about 1/2” depending on spring condition). Beyond 6”, the stock driveshafts start causing problems for highway usage and offroad with the amount of axle droop that you can achieve, primarily in the front. There is a reason why most Samurai lifts are between 4.5” and 5.5”.

The rear driveshaft U-Joint angles become so miss-matched that you will start experiencing constant vibration at highway speeds. At low speeds, the T-case shifter will act like it is trying to come through the floor when rolling through second gear or under hard acceleration in any gear. On my personal truck with 8” of lift, I was going through a U-joint every three months at the T-Case rear output shaft and the rear lower pinion joint about every 6 months.

In the front, you simply run out of driveshaft droop as the upper T-Case U-joint yoke will bind on itself or the slip yoke body will hit the cross member. Both will occur at nearly the same point, so simply grinding out the yoke or cutting out the cross member isn’t going to help to any significant amount.

Drive shaft spacers, extended slip yokes, or modified length driveshaft tubes, work great to add needed length, but none of these do anything to address the U-joint angles or binding when going with over 6” of suspension lift. A lot of vendors never mention this to their customers. We have seen written ads by one vendor for 7” and 8” SPOA suspension kits that include big 1.5” spacers to “correct perfectly for the lift height and allow for maximum flex on the trail”. They also state “This suspension system not only makes your vehicle look like an offroad monster, it performs like one as well”. There is probably more truth in that statement than meets the eye. I run an 8” lift suspension (not theirs!), and believe me, without addressing the driveshaft problem, you would have a real MONSTER on your hands!

With 8” of suspension lift and the truck parked in the driveway, the front driveshaft would be very close to being locked up at the T-Case. The rear U-joint angles would be so mis-matched that there would be a tremendous amount of vibration in high range. The stock driveshafts just cannot tolerate such angles, and they were never designed to. Basically your truck would be unusable except for smooth highway usage. We don’t sell driveshafts, so this isn’t some sales pitch to sell you one. It is intended to provide you with the truth as to what you should expect. If your going to go big with over 6” of suspension lift, then you need to budget for a pair of aftermarket driveshafts.

A lot of people will combine a suspension lift with a body lift. For liability reasons, none of the manufacturers of body lifts or suspensions recommend this practice, so neither can we. Body lifts do just that, they lift the body away from the frame providing additional tire clearance. They do not provide any advantages that are realized from a true suspension lift, nor do they have any impact on driveshaft angles. You have to decide what is right for you and your budget.

The most popular body lifts are the 1” and 2” versions. The 3” body lift is more difficult to install, and causes problems with the fuel filler neck hose, and the clearance in the body pan for the transmission and transfer case shifters. A lot of people also do not like the large amount of open space visible between the frame and body, but this could be filled to provide a visual barrier.
-------- From "6 Inch Rule" - NorthcoastOffroad -- a site that is now history...

Man am I glad I came here.First question would be, can you roll the axle assym. to accomendate the extra pitch of a large lift? Cut and reweld spring mounts, shock base, extend brake lines. Then you might have to shorten the drive shaft. I've done this on a monster truck, so I would feel comfortable with it. Dont really like to run what everyone else does, I am not much of a painter, so all the character for my little monster pretty much comes from the tourch. I do want to be able to sport my lil monster around town. So I will maul all this very good info around and we will see what the end result is.

Thanks

From your other post you said you are building a sidekick, right? 
A samurai and sidekick have 2 completely different suspension setups on them (leafs vs. coils).  With either one, you are going to be hard pressed to run 8 or 9 inches of suspension lift, and get it to work at all (especially on a trackick).  My suggestion would be, for either one, is to cut the fenderwells as much as possible, to clear the tires, and go with as little lift as possible.  With 12" of lift, your center of gravity (COG) is going to be so high, it will basically roll over in a strong crosswind (maybe a little bit of an exaggeration, but not much).  If you are building a sidekick/tracker (trackick), then there is really no way to run 8" of susupension lift, unless you do a straight axle swap (SAS) on the front axle.....stock CVs simply won't handle that much lift.  On samurais, guys run 34" tires with less than 12" of total lift....as mentioned, there is some fender trimming, and other stuff involved, in order to pull it off.
I am not bashing your ideas, I am simply stating the facts, and trying to keep you from wasting a lot of time and $$$.

skyhi beat me to the punch on my suggestion sas is the only way to go for that much lift

We moved the floorboards on my son's side kick back 3". Wazn't really all that difficult to do. Gimme a bit and I kin mebbe find some pics of it.