Just wanted to post this because it always drove me nuts having red stitching everywhere else in the car besides the shifter and e-brake boots. Here is a simple solution.
Total Cost- A couple bucks!
Here is a guide for WRX's and STi's on how to remove the shifter and e-brake boots. The guide says 14+ WRX/STi's, but it applies to early years as well.
Subaru WRX 2014-15 shift boot installation - RedlineGoods leather shift boot store
Use a hairdryer to loosen the adhesive of the e-brake boot and slowly peel it from the plastic. After you are done with the stitching use a 3M Adhesive Spray to glue it back to the plastic frame. The shifter boot simply comes off and doesn't need any of the special treatment the e-brake boot calls for.
For the stitching I went up the boot skipping a loop the entire way up and then went down filling in the missing loops. Easy! Don't worry if the inside of the boot looks a little messy. Just focus on making sure the outside is straight and pretty. Mine isn't PERFECT, but I am more than happy with it. At eye level in the car you would never notice any imperfections. It has held up very well in the 4 months I've had it in the car with everyday use.