A you tube video I saw suggested that there are improvement for 'SE' models.
Please tell me that you have not fallen for the composition or manufacturer of a non-polarized cap affects tone myth. Capacitors are linear components. What "linear" means is that capacitors operate in straight lines according to the equation i = C * dV/dt, where i equals current, C equals capacitance in farads, dV equals the change in voltage, and dt equals the change in time. Any capacitor that does not behave in this manner is considered to be defective. The only way two different non-polarized capacitors with the same rated capacitance can result in a difference in tone is if the capacitors have different measured capacitance values. For example, polyester film Type 225P Orange Drop capacitors can have tolerances as high as 20%; therefore, two caps from the same manufacturer can have substantially different measured capacitance values. A lot of people purchase from Mouser. Mouser sells the 10% tolerance version of these caps, which means that a Type 225P 0.022uF cap from Mouser can measure as low as 0.0198uf and as high as 0.0242 and still considered to be in spec. That is a difference of 0.0044uF or 4.4nF, which is enough to affect the how the tone control responds when rolled all of the way down. Additionally, the tone cap in a guitar does not shunt or pass frequencies. What it does is combine with the distributed capacitance in the pickup coil(s) to lower the circuit's resonant frequency (see my "Delving into TCI" post for an explanation of how capacitance affects resonant frequency). The fact is that there two types of people who propagate capacitor myths; namely, those who aim to make a buck from higher-priced caps and those who have been taken advantage of by those who aim to make a buck from higher-priced caps. If two capacitors with the same rated value result in a difference in tone, then they need to be measured with an LCR meter. I guarantee that they will have significantly different measured values.
The PRS core pots are not standard CTS pots. I believe that they are custom CTS-manufactured copies of the old CRL/CentraLab pots that Paul used during the early days. CRL/CentraLab audio/log pots have a faster taper than standard CTS pots, which is great for guys who ride the volume control(s) on a PRS. The pots used on the SEs are good pots. In fact, many boutique amps use Alpha pots. Another thing that needs to be considered is that Alpha pots are 8mm metric, CTS pots are 3/8" imperial, which means that you are more than likely going to have to take a reamer to the guitar to enlarge the stock holes.
There is no such thing as voodoo wire either. Heck, wire diameter does not even factor into the equation at audio frequency. Given that it is sized to current load, wire diameter does not seriously come into play until one hits radio frequency, which is where the "skin effect" comes into play.
The nut is about the only area where one achieve a big bang for the buck on an SE. A core nut is not that expensive. Locking machine heads (a.k.a. tuners) are a nice upgrade because they make stringing a guitar much easier. An improvement can be achieved by changing the bridge, but I do not think that the cost warrants the improvement. The CE24 I recently acquired new has an import trem. I thought about upgrading it to a MannMade trem because I discovered that the ball ends tend to stick in the block when I set the guitar up for 9.5s. I do not recall that ever occurring with my '95 Standard 24 or '11 Custom 24. It is a minor nuisance.
The moral of the story is that you should play and enjoy the guitar. If a pot wears out, replace it with another pot. The same thing can be said about the switch. However, replacing everything on an SE can rapidly raise the cost of the instrument to that of a nice used core Stevensville guitar.
