I think I'm going to end up with the exedy. The clutch doesn't know what motor so I don't see how there could be an issue there. There are plenty of guys with super charged 3.4 motors making 300 plus ft lbs of torque. I never had issues with a properly matched exedy years ago with my turbo Honda B series.
What issues are you having with your clutch?
I have the same motor, same tune in my 5 speed converted passat.
I started with a a clutch master fx300 clutch that was far from cheap. Started slipping in less than a year of daily driving. The pressure plate had failed, lost all clamping force. The clutch flywheel set up was some 1000 bucks or more. I was far from thrilled. They had me ship it to them to see about warranty then informed me weeks after having it warranty was 90 days. Sadly we discussed purchase date in email/phone calls several times before I removed the assembly to ship it to them so they wasted both my time and shipping costs. I will not deal with them again. They could have informed me of the warranty period before I shipped.
I then switched to a valeo stock 220 mm clutch found behind the 1.8t gas motor. I sent it off to South bend for there endurance treatment. Less than 700 bucks in the clutch/flywheel/treatment.
Much more friendly daily driver with stock clutch feel but it is very very grippy so in a rig off road it wouldn't be very smooth while feathering the throttle/clutch to get over something. You pretty much engage the clutch or don't otherwise she'll chatter and shake the car if you don't feather her properly. She's been slip free for going on 2 years and some 50k miles now.
With the larger diameter of the 3.4 flywheel it might engage a little more smoothly as it has more surface area? So a stock aisin with endurance treatment at south bend might be a pretty good option. I'd just hate to install it and it suck off road. The crawl ratio of the 4 runner with 4.10s and 33s isn't very good. I don't spend much time off road but when I do I like to have fun driving it.
About 8k km after the swap I started to notice it was getting harder to change gear, so I replaced the old master and slave cylinders and reinstalled the factory accumulator. None of this solved the problem, and I would occasionally have the clutch completely fail to disengage when I pressed the pedal. I finally discovered that the clutch fork was positioned very near to the rear of the opening in the bell housing, causing it to chew up the rubber boot, which was limiting its travel. The only way I can see this happening is that the springs in the pressure plate have "sagged" over time, causing the slave cylinder to extend farther and pushing the clutch fork closer to the edge of the bell housing opening. I had no troubles with this for at least 6000-8000km.
This is the clutch in its resting or engaged position, pedal not depressed:
I also have experienced clutch shudder in first and second gear since day one. I go off road fairly often, so the shuddering has definitely been an issue, coupled with the on/off nature of this clutch. I'm running a Malone Stage 4 tune with around 275ft-lbs and don't plan to go any higher, so longevity and drivability are more of a concern that high performance. Sounds like I should look into the CTX-107/DTX-136 setup.