I have had a lot of time to think about this problem recently. After I started modding my Exige S for the track, I shattered my stock clutch disc (admittedly at a VERY high-speed/open-throttle circuit). Replaced it with an ACT HDSS setup, then over the course of the last 2 1/2 years went on to grenade TWO transmissions (both 3rd gear failures), the ACT SS clutch disc (one of the hub springs broke free), and most recently, the ACT HD pressure plate (broken pivot ring).
Along the way, I did several mods that in all likelihood reduced the reliability of the drivetrain: 1- sticky R-compound tires, 2 - more aggressive brake pads, 3 - Increase in power and torque, 4 - HD pressure plate, 5 - multi-clutch type LSD (bought it because it locks up on decel, making the car more stable under hard braking). Oh, and a crazy aggressive driver on the track. All of these mods increased the magnitude of potential torque spikes to the drivetrain.
And it might not be just acceleration and upshifts that are causing the problem. I am a very late braker, and I think this can be very hard on the drivetrain during high-deceleration downshifts with braking. Granted, the gear tooth sizes on the C6x transmission and strength of the clutch assembly were all designed for the NA Celica GTS open-diff front-drive platform (which is to say, not nearly beefy enough), but anything you do to increase grip, engage the clutch faster, and insure rear axle/diff lock-up only increases the stress in both acceleration AND deceleration. BTW, going to a solid clutch disc would only make the situation worse, as the hub springs are there to soften the engagement and mitigate the torque spike when the clutch is released. In many of the newer German cars, this is what the "Dual-mass" flywheel (really two flywheels connected by elastomers) is for.
It is starting to make sense to me that Lotus never sold a 2ZZ/GE-C64 street car with more than 260hp and only a torsen LSD (which doesn't lock up on decel) as an option. And even fitted the clutch delay valves to those higher HP cars.
So the only advice I can add at this point is to also look at your downshifts under braking and try to let the clutch out more slowly. That's what I'm going to try to do next year. And assuming we don't want to reduce tire grip, brake grip, or HP/torque, maybe resign ourselves to the fact that the clutch should be the "fuse" of the drivetrain. I think some guys are switching to a pressure plate which has a clamping force closer to the stock Toyota unit, which might allow more slip in the case of a big torque spike. I can tell you although it's a pain to replace the clutch, it's still a lot easier and cheaper than rebuilding the gearbox (again)...