Hi mate,
I've run both an S53 and S54 in my ST162 with a rebuilt 3S-GE. It's by no means a 'power-house', though it was dyno'd at around 130hp through the front treads. From my experience, the S54 is a nicer box. Mine wasn't a very new box, but I believe it had very little km's on it when it went in.
In saying that, my S54 is now crunching 1st>2nd (unless shift real real slow and rev-match), 4th>3rd and 3rd>2nd. I haven't driven my car overly hard, always make sure I an extra nice to the gearbox and change oil when required.
The S53 was buggered when I got the car, then I rebuilt the engine and put the S54 in. I'm about to go for my 3rd gearbox now.
I can only recommend finding the latest model S54 you possibly can and using that. It will inevitably wear out, especially behind a 3S-GTE.
Another option to think about could be the gearbox from a 1MZ or 3VZ. A lot more work involved compared to the S54, though it would withstand the torque that the GTE will throw at it!
Also I believe a later model box (maybe from the FWD beams packages) came with double syncro's on 1st, 2nd and 3rd. I am yet to comfirm this, though if it's the case, that's what I'll be looking to install in my ST162.
Cheers,
Al
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