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Depends on the trans you used. If you used the R154 (stock in both the 7M-GTE and 1JZ-GTE 5-spds) then you use the 1JZ-GTE flywheel and bellhousing and the clutch is the same as the 7M-GTE's as the only difference in the flywheels is the bolt pattern drilled in the center to bolt to the crank. This means a 1JZ-GTE swapped car can use any 7M-GTE clutch if it has the R154 5-spd.
If you used a Getrag 6-spd (twin turbo MK4) then you would use the 2JZ-GTE clutch and flywheel from a TT/6-spd MK4. The 6-spd conversion requires a good ammount of modification to the shifter bracketry to fit in the stock MK3 shifter location, as well as a custom tranny mount, drive shaft, and some method of changing the rear differential in the MK3 to suit the 6-spds gearing, stock US MK4's came with a 3.13:1 rear diff ratio, so even the numerically lowest stock MK3 diff with a 3.73:1 is far from ideal. Most people stick with the 5-spd because of this.
You could also use one of the NA 5-spds but you'd need the appropriate 2JZ-GE bellhousing for it, and you'd use a clutch for an NA MK4.
So its not a matter of what "runs better" as much as of a matter of what you used dictating what you'll need. With the revvy nature of a 1JZ-GTE they respond to lightweight flywheels and driveshafts very well from what I've heard.
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1995 black/black SE Hardtop, USDM 2JZ-GTE/Getrag swap, singled, fuel, triple disc, Kaaz, brembos, sparcos, racelogic blah blah blah
1987 silver/grey - 7M-GTE *was* 399rwhp/428rwtq
1991 LS400 white/grey - ballin daily
1991 MR2 Turbo 5-spd (sold)
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