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E46 coupes are lookers still, and well kept stock-ish examples are harder and harder to find. So on that note: if anything, manual swap it (if I’m reading your post correctly and it is currently auto) and find a higher ratio limited slip rear end if it doesn’t already have one. The 6 speed isn’t necessary, the 5 speed ZFs are stronger, more plentiful, cheaper, and are functionally identical (the 6 speed is basically the 5 speed’s ratios plus a .81 overdrive).

You’ll spend a dumb amount of money on doing internals and the M54 will never make more than 250hp. It’s just not worth the cost. If you really want power, try to find a used supercharger kit. The M54 is a delightfully smooth and torquey motor, not a powerhouse and not built for high rpm/high stress track work, so my recommendation is to put a decent exhaust on it and enjoy.
 

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Chase Bays has a pretty extensive guide for what it takes to swap a 2 or 1JZ into a BMW.

why bother when the N54 is a direct mechanical fit? with a port injection adapter, upgraded in-tank pump, and a single turbo conversion with a fat FMIC they put down a conservative 600whp all day long…. and way more on corn juice or if you spring for a 5-axis VAC Motorsports head to spin it up damn near to 8000rpm.

BMW tuners have come a long way with cracked DMEs and custom tunes. 2JZ is an inferior option and wildly more expensive than an N54 from LKQ… they came in hundreds of thousands of BMWs over the past decade+.
 

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My recommendation for the eventual manual swap is to either find someone with a lift and a transmission/engine removal jack, or to buy one of those MaxJack things. The ZF 6 speed came on dozens of models throughout the years, so don’t worry about finding an E46-specific one (8cyl has different bellhousing).

You’ll likely also need a manual-transmission driveshaft (the auto trans is a different length on a lot of BMW models. I may be wrong, though, about the E46). That means you should also buy a new giubo/flex disk and center support bearing.

Also find a limited slip differential.
 
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