Nothing wrong with an off-the-shelf JWT tune as long as you make sure everything's working correctly. I made 462whp on my stock JDM DE with Tomei cams, log manifold, BB 0.82A/R/60-1 turbo at 23psi (IIRC, something sane like that), and some C16 mixed in for good measure. Only thing I changed was switching to 20* base timing to take advantage the race fuel and clear up some misfire I was seeing.
Could I have made more? Sure, but that car survived for a long time (motor's still good, car just hasn't been registered for a while due to CA smog issues) even running that level of power hotlapping (basically, WOT for 20 minutes straight). Hell, way back when, at the LA convention, I ran the track event, did some drag racing, and drove the car everywhere that weekend, no problems.
That being said, I wonder how far I could've gone with a custom tune. At this time, however, I've got way too many projects to pursue, and when the SE-R sees street duty again, it'll be with a far more sane setup. A powerband that doesn't start until 4500rpm, then slaps you in the face with wheelspin in EVERY gear, while fun, just isn't my cup of tea anymore, especially since I don't want to spike with race fuel all the time, or build a motor.
BTW, not sure if this was already addressed (read the first 5-6 pages, then the last 3-4 pages), but the stock knock sensor is nearly worthless at higher power levels. As I recall from back in the day, JWT said their tune ignores knock sensor input on the larger injector setups because it gives too many false readings.
Also, I was just at JWT a couple of weeks ago dynoing a buddy's car, and Clark was saying the VE's have amazing knock resistance. The car we were dynoing had the MAF get dirty in the middle of the session, and A/F went to 17:1, but we never got a knock count, nor did we hear anything other than the motor sounding a little unhappy. He was saying these motors like a little lean at higher RPM, and you can get away with a lot more aggressive timing/fuel curves on them compared to DE (which would explain all the big power you guys are making on pump gas).