First off, I must give anyone reading this a disclaimer.  SOAs are a huge change to your Jeep's suspension and steering.  I do not recommend anyone performing an SOA conversion unless they fully understand the ramifications of this type of lift.  I could tell you about how raising your center of gravity will increase the possibility of a roll over and other such safety rhetoric, but if you're far enough along to consider doing an SOA on your rig, you already know this.

This is only my experience with Wrangler (YJ) SOA conversions.  Besides my own, I have participated in two other SOA conversions.  I also have two other friends I wheel with that have SOA conversions on their YJs.  I have never participated in an SOA conversion on any other vehicle.  This is not to say they cannot be done, just that what you read here may or may not apply to your particular situation or vehicle.  I'm not exactly sure about the costs, but I know I had $600 set aside for it and it was gone when I was done.  I know they can be done cheaper, but I'm not sure if I would skimp on anything.

Spring Wrap

Probably one of the biggest problems with an SOA conversion is spring-wrap (a.k.a. axle-wrap).  Spring-wrap is where the axle, torqued by the driveshaft, is attempting to rotate and twist the springs around it.  Normally the springs would prevent the axle from rotating and instead the tires would move forward or rearward.  Spring-wrap can occur on SOA or Spring Under Axle (SUA) vehicles, but appears to be more prevelant on SOAs.  An immediate symptom of spring-wrap is wheel hop.  There are a few ways to cure this problem.  A good spring pack, anti-wrap perches or traction bars are a few.

Spring Pack - Stock springs, with an add-a-leaf of some sort, are generally the spring packs used in most SOAs.  I'm using the stock front YJ spring packs (front and rear) with Rancho 2" full length add-a-leaves.  The Rancho full length add-a-leaf is very stiff.  This aids in preventing spring-wrap and also helps to fight premature spring sag which is also common among SOAs.  Mine is the second SOA I'm aware of with the Rancho add-a-leaves.

My friends have tried other add-a-leaves with varying degrees of success.  National sells an add-a-leaf that's full length like the one from Rancho, but a much softer spring.  MIT uses them in their SOAs.  None of us have had much luck with them because they're so soft they sag prematurely.  The Procomp add-a-leaf just plain doesn't hold up.  It's too short so it does nothing to fight axle wrap.  A Jeep with us on the Rubicon broke both rear add-a-leaves on that trip.

Another spring pack configuration I am aware of is stock springs with an additional stock spring added in the pack.  The eyes of the longest spring are cut off and added to the pack.  I mostly hear of premature sag with this configuration.

Another option is to use lift springs.  Myself, anything more than 2" would be too much, unless you're going to put tires on larger than 35".  I am unable to make a judgement on the durability of lift springs in the SOA configuration.

Perches - To help fight axle wrap, I used the RE anti-wrap perches.  If you could get your hands on a set to look at them and measure them, they'd be real easy to manufacture instead of the $75 they'll cost you.  The perches are very beefy and the fronts are offset so you can clear the pumpkin and axle disconnect housing.  If you go into a 4x4 shop and ask for perches, they will give you an identical set to what you currently have on your rear axle.  We have used these, but on the front axle you will have to grind the arch on one side of each perch to make them sit level on the axle because of the pumpkin and axle disconnect housing.  Two the the SOA YJs I wheel with have even re-used the front perches.  They cut them off and swing them up to the top.

Driveline - On the front perches, you'll want them welded parallel to the stock perches underneath.  On the rear perches, it will depend on your driveline setup. The rule of thumb is, transfer case yoke parallel to pinion yoke except after CV.  In my case I use a slip-yoke eliminator on the NP-231 and a CV.  So I must point my pinion at the CV.  This is without question the better setup than using a transfer case drop and 2.5 degree shims on a YJ.  But those are your choices.  Below left is a picture of the MIT slipyoke eliminator  and the CV.  Below right is a picture of my pinion yoke and driveshaft.  Notice the pinion yoke is pretty much inline with the driveshaft.

Steering Geometry -  Another problem to overcome with SOAs is the steering geometry.  The angle of the draglink is of specific concern.  When the draglink is positioned in severe angles it creates bumpsteer when going over bumps.  When the suspension compresses and the axle moves up so does the axle end of the draglink.  This in effect lengthens the draglink and pushes on the pitman arm.  This translates to the steering wheel as movement.  It can be a frightful experience at highway speeds.  Although, some claim to get used to it and adjust their driving style.

For the steering I used a stock pitman from a ZJ which is the same as a drop pitman for a YJ that a 4x4 shop will sell you (except about $30 cheaper).  Bud had an extra drop pitman for a CJ that we tried first.  The CJ drop isn't quite as much and the alignment of the keyways is just a bit different.  It fit but it didn't work well.  I already had the drop draglink from MIT.  I put the drop draglink in a long time ago because the drop pitman was hitting my tie-rod bar.  So when I had the Superlift 3.5" and the Procomp 4" I used the stock pitman with the drop draglink.  As far as I know, MIT is the only one making these.  MIT does a lot of SOAs so talking to Jeff before you start is a good idea no matter what you decide.

Trac-Bar or Panhard Bar - Many people remove the trac-bar from their Wranglers.  In almost 100% of Wranglers that are regularly put on the trail, the rear trac-bar will be removed permanently.  It's a good idea to remove the front trac-bar off-road.  However, on the pavement is another story.  The trac-bar is intended to keep the axle lined up under the Jeep's chassis.  For stock or moderate lifts this certainly isn't as crucial but on an SOA Jeep there will be a lot of movement of your axle without a trac-bar.  The types of things you will feel on an SOA without a trac-bar is slow steering response and a tendency for wander, especially under heavy breaking.  The problem with mounting the trac-bar with an SOA is similar to the problem with the draglink.  The more angle the less effective it becomes.  In some cases, it can actually make things worse by causing your axle to shift on bumps if the angle of the trac-bar is too severe.  Ideally, you will get your trac-bar back to stock angle.  There are extensions sold with many lift kits.  I would stay away from them.  The rear trac-bar extensions are almost guaranteed to tear the stock mount and it can also occur in the front.  Although I have only seen one actually tear the mount in the front.  The tear was in the cast gusset on the mount.  What I did was steal MIT's pattern.  I have it pictured below.  It is simply 3/8" steel plate welded to the spring plate.  A hole is drilled and the trac-bar is bolted on.  I've welded a nut on the back of mine so I don't need two wrenches to disconnect/connect the trac-bar.

Shocks - Lower shock mounts can be a slight problem.  Naturally you want as much travel as possible, but you don't want to eliminate clearance under the axle. I cut off all of the stock lower shock mounts.  I couldn't find the right size U channel but did find the right size square tube.  I just cut one side out of the tube, drilled a hole for the shock bolt.  I then rounded the side of the mount that was to be against the axle and welded them as low as possible on the axle housing.  On the front shock towers, I installed the upper shock mount conversions from Rubicon Express (pictured below).  These convert the top mounts to an eye instead of the stud that is stock on YJs.  This allowed me to mount my shocks upside down.  We've had a problem with some of the SOAs beating the shock canister on the springs during articulation.

Brakelines - I use extended brakelines from my previous lifts and have re-routed the front lines under the frame.  You must use very long brakelines in the rear.  For the emergency brake you can buy extended lines (although I have no idea where) or you must re-route them.  For the passenger side this is simple.  Just disconnect the line from the mount near the exhaust, move it below the mount and that pretty much takes care of the passenger side.  The drivers side doesn't have enough existing length or slack for anything that simple.  But there is a little trick.  Disconnect the driver side emergency brake line at the adjustment contraption.  Drill a new, lower hole for the break line mount and reconnect it.  I would recommend gusseting this bracket.  I haven't and as you can see below, it is bending.

Misc - Check everything going to your axle for adequate length.  In particular the differential breather hoses and also the 4WD axle disconnect on the front axle.  There is without a doubt, not enough slack in these lines if you do nothing.  However, it's just a matter of a little re-routing to solve the problem.

Other sources of SOA info:
http://www.off-road.com/4x4web/jeep/reviews/rubexpress.htm
http://www.off-road.com/jeep/tech/susp/cjsoa.html
http://www.mswin.net/users/cuetips/jNotes.htm#suspension
http://jeepskate.4x4.org/SOA.htm
http://www.off-road.com/jeep/tech/convaxle/fordeb/soa.html