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The ecu and tcu are both flashed separately. Your tune would not affect anything in transmission.
I'm running a 4.88 for about 8 months now. I drive it hard and have had no issues.
You might just have a bad transmission.
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2013 Whiteout 6AT FR-S | Perrin Inlet Tube + 2.75" CAI | OpenFlash Header | P&L Catback | 4.88 Final Drive | Dialed in OFT 2.0x Stage 2 E85 | 18x8 Enkei Raijin + 225/40 Michelin Pilot Super Sport | 17x7 Stock + 215/45 Michelin X-Ice Xi-2
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