Okay, here is a short account of what modifications I did with my new Jackson SLATFXQMG 3-8 TGR. First of all, I installed Schaller Security Locks as a replacement for the strap lock system that comes with the guitar. I did this only for one reason: I have the same locks on all my other guitars and I like to use any strap I own with any guitar I own.
The stock guitar comes with rather thin strings, so I replaced them with a combination of DDT7-11 strings (11 15 19 32 42 54 65) and a Warwick longscale roundwound bass string (80). I tune my guitar to EAEADGBE, where the additional two strings are tuned to an octave below the 5th and 6th string. In order to be able to fit the 80 string, I had to widen the hole in the 8th string tuner. Since I use thicker strings that the stock version, so I had to adjust the intonation, where again, I had to remove a part lower left edge of the 8th string slider.
The most subtle modification that I did is the well known 18V mod that gives the EMG pickups a little more headroom. And then I did this: I removed the tone pot from the circuit, removed the capacitor. I added a 1 uF capacitor after the tone pot to the signal line and then after soldered the tone pot in series with a 160 Ohms resistor to the ground. This turns the tone pot into a variable low-cut (high-pass) filter, which can be used to clean up the bottom end, resulting in more mids and tighter bottom with overdrive/distortion sounds.
(I also splashed some additional color on the guitar :))