Welcome to the site.
I leave the tuning to my tuner.
There are many threads on several sites by people " tuning " their own cars. If you don't know what you're doing, it's very easy to hurt your motor......good luck.
Get a Cold Air Intake / Tuner Combo and you will NOT be disappointed...I have the JLT / SCT with a Bama Tune and am real happy...At least get mufflers so the 5.0 sounds it should (American Thunder Flowmasters work for me!)..
Make sure you go through a reputed tuner and make sure your effectively communicate to them what you want.
I have a bolt on CAI that whistled when I put it on. After my tune, no more whistle! I recommend proper tuning when changing anything that has a sensor in it on EFI cars.
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Have never used a canned tune, but understand they are on the conservative side, from reading posts on several sites. A lot of people like them, but with my mods, they won't get the job done.
I would recommend a remote tuning session from one of the reputable tuners. It is more expensive than a canned tune.....but with remote tuning...it's done in your environment, on the road or on a local dyno, using your fuel. I data logged on some backroads and the car was dialed in for my specific mods and yet it's a very safe tune. I think canned tunes serve a purpose....but it would be extremely difficult to build a canned tune that compensate for all altitudes, fuel blends, idiosyncrasies of each engines etc. and the more mods you do...that complicates things more.
I'll give you one very specific detail that outlines how precise the remote tune can get. I purchased my remote tune session and sent the list of mods for my base tune. One of the upgrades was to be the PJ carbon fiber AirAid intake for my Boss. I ordered the intake just prior to ordering the tuning session. AirAid had an indefinite backorder...I found out two days later.....so I ended up with a plastic version that could be used on either the Boss or GT. They look very much similar when sitting side by side. Anyway, I did my first session of data logging and sent the files to the tuner. He immediately emailed me and said the I did not have the carbon fiber intake installed....he said he could tell by airflow ratio's. The carbon fiber flows better...but doesn't yield any additional power...he just needed to adjust fuel trims. I'm not sure a canned tune would get specific enough to make fine adjustments...such as whether one has a plastic version or carbon fiber intake.
So the Bama tunes aren't necessarily canned tunes. True, they start off as a "canned" tune to get you in the in the ballpark... but I recall reading in the fine print that after you receive your "canned" tune they recommend data logging with several 3rd gears pulls then sending the data back to them and they will tweak it so that it's personalized to your mustang.