You Just asked a HUGE question. Preparation for a tune all depends on how much HP you want to make, what your end goal is, and whether or not you will be adding more parts to the car later down the line. With only having 6k on the motor right now I wouldn't recommend a tune just yet simply because it requires MANY WOT pulls throughout the tuning process to dial things in (that is if you are going with a custom tune). Your engine needs a little more break in time before all of this abuse. Some say this is just a theory, but look in the owners manual of any newer car and it will state sometime like "do not race the engine for X number of miles." Normally around 10K.
Some tuners will recommend colder plugs while others don't. Even if colder plugs aren't required, many tuners will ask that you close the gap on your plugs to 0.026 - 0.028. The ST's plugs are gaped to 0.030 from the factory. I know this because I played with plugs a lot during the tuning process. Unless you are going big turbo or trying to make big numbers, colder plugs aren't necessary.
Now I've been through a lot with tuning. I started with Randy from Mountune because he include a tune with the AP. Be careful with this. This is not a custom tune but rather a flash tune that the tuner makes small tweaks to with fuel and spark adjustments. Depending on the gas you have available to you, a flash tune most likely is not your best bet. I would highly recommend a full custom tune for your car to avoid negative ignition corrections and unnecessary knock during and after the tuning process. This will make for a much safer tune and make the engine of your car last a lot longer.
The most important thing you can do at this point is educate yourself. Make sure you understand what is happening with your car before the tuning process begins. This was the mistake I made, and I ended up learning everything along the way which caused me to make mistakes. I would heavily monitor Negative Ignition Corrections during the tuning process. The short version is negative corrections = engine knock. It's much more complicated than this, but at the end of the day you want to be as close to zero or only positive if at all possible. A good tuner will understand this and make sure you don't harm your car. If you learn all of this ahead of time you will know exactly what to look for during the tuning process.
If there are any "tuneable" items you would like to add to the car, it's a good idea to do those first. An intake, intercooler, bigger turbo, exhaust, etc. are all items you can achieve more HP with through tuning. Don't get wrapped up in "Stage 1,2,3." Those honestly mean very little and are only referring to a grouping of specific modifications to the car. Other items that don't directly affect fuel, air, or spark, can be added to the car later on without having to make adjustments to the tune (such as a rear motor mount). Most tuners will require you pay an additional fee if you want to make adjustments to a tune once it's finalized, so if you buy an intercooler down the line you may have to pay again to re-tune for that specific part. Some tuners will offer a "lifetime" tune as an option. Usually these "lifetime" options are more expensive, but cover you for any additional parts you add to the car in the future. Some of these tunes are upwards of $300 - $500, and don't forget about the cost of the Cobb AP which is about $500.
Stratified is a good option. Their tuning process is long, and VERY thorough. This is a good thing. Just remember they are in British Columbia, so any phone calls will be long distance, and and shipping of parts etc. will be more costly. Most of the time this isn't a problem. I would suggest you take a look at "Purple Drank" tuning. Yes... that is the actual name. I was skeptical at first myself, but these guys are NO joke. I went from pulling LOADS of negative ignition corrections with my first tuner, to absolutely none in one tuning revision with PD. The work they do is extremely underrated, and the service is top notch. Ryan Martian was recommended to me by another fost.org member and I gave him a call. He has answered my phone call every single time I've called him. He sends me revisions to my tune quickly, and my car pulls so freaking hard. Don't pass these guys up as an option... and remember to do your research. Don't just read the reviews on the company page, but rather search around and make an educated decision.
I would recommend an intake (or just a drop in filter), intercooler, and RMM (to combat engine rocking from the added power) before the tune. These aren't absolutely necessary, and if you don't want to drop the cash on a bunch of parts up front make sure you get the lifetime tune so you can add parts to the car without having to pay to re-tune later on. At the end of the day all of these decisions are up to you. Also remember that EVERYTHING I just typed can and should be discussed with your tuner before hand. You should be able to discuss your power goals and have a road map going into this thing. If you can't do that, you shouldn't be tuning with that person.
These are just my experiences, and I hope this helps.
--Bradley--