The stock pickups are actually quite decent, especially for a guitar in this price range, but weren't quite what I was looking for. The neck pickup (which I use the most) is full and has a fair range, but lacked the clarity and note articulation that I like. The bridge pickup is one I rarely use by itself. Although the stock one was adequate, I found it a bit thin-sounding. This is not a put down of the stock pickups, as they are quite useable. However I've never been one to leave well enough alone in the quest for tone. With the new pickups and electronics mods, this guitar sounds amazing. I've used Duncan pickups a lot, and in this guitar with it's mahogany body, they really come alive. The Jazz pickup in the neck is exceptional and I have a full review of it here in the Harmony Central user reviews. The combination of both pickups is also excellent. However, the electronics mods have made a world of difference. The 3-way mini toggle switch is set up so that in the down position it's in series, which is a full humbucker sound, in the middle it's split, which is single coil mode, and in the up position it's in parallel which sounds kind of like a combination of single coil and humbucker.
This mod has opened up a world of tonal possibilities, and some unexpected results. I was most surprised by the single coil mode. Since I wanted a humbucker guitar, I didn't think I'd get much use out of the single coil sound, but it sounds incredible. Not quite like a Strat, but the tone could be described as glassy, crystaline, and almost like an acoustic-electric guitar - very sweet. Another surprise was using the middle position of the guitar's pickup selector (both pickups). I've never used this position much on other guitars, but with these mods, the guitar has an unbelieveable tonal range. By the way the electronics work was done by Griblin Engineering (www.griblin.com) who has a a lot of cool custom electronics parts available on their website.
I play a pretty broad spectrum of music, from "classic" rock (Hendrix, Santana, Jeff Beck, etc) to jazz-funk, to ambient electronic and this guitar covers it all. The neck pickup sounds really great with an E-bow. This one is the newest guitar to my collection which includes a Gibson Les Paul, Fender Strat w/ built-in Roland synth pickup, 72 Telecaster Custom, and Fernandes "Sustainer" guitar w/ Roland GK2A synth pickup. All my guitars have non-stock pickups - Seymour Duncan, Lace Sensors, etc. I mention these, because out of all of them, the Santana SE II (with the mods) is the best sounding guitar I have.
I've been doing more recording lately than live playing and generally go direct into the board through a Mesa Boogie tube pre-amp. Although for gigs, I run a stereo rig with lots of effects into a Mesa Boogie Studio 22+ and a Fender Blues Jr. The guitar interacts well with my effects and the sound coming through the stereo set-up is amazing and totally exceeded my expectations. I know I've been talking about a fairly hot-rodded guitar, but the stock Santana SE II sounds quite nice in it's own right and compares favorably to my Gibson Les Paul.
I've had the guitar for over six months and it certainly seems durable. Like I said, I haven't been gigging as much lately, so I don't have a lot of tales from the road, but I can't forsee any problems with it's reliability. However, I would never play live with out a back-up guitar, no matter what main guitar I was using.
I'm in my mid 50's and have been playing guitar for over 30 years. I've owned a lot of great equipment, including pre-CBS Fenders (which I wish I still had). I won't say that this is the best guitar I've ever had, but I would rate it highly and say that I am very happy with it. It's an excellent moderately priced guitar that responds well to upgrades and is the best sounding guitar I currently own, after the mods. I'm comparing to my other guitars which have also been upgraded, so it's a fair comparison, in spite of the fact that the Santana SE was a less expensive Korean-made guitar. Like I said, I bought this particular guitar to work on, but I could have been happy with it in stock condition also. I have been a huge fan of Carlos Santana since the 60's and he has been a major influence on my playing, so having his name on the headstock was kind of like the cherry on the top. I know that the SE has little in common with the American-made PRS Santana, but it also doesn't cost $3000 or more. I also checked out the PRS Tremonti SE and liked it, but not as much. All in all, this a well made, reasonably priced guitar that covers a lot of bases, and one that I would highly recommend.