I'm actually running an M54 Z4 3.0i 6 speed in my S54 E30 M3.

Fitment wise, I don't think the S54 is meaningfully different from an S52 swap. I think it's likely actually easier than an S52 electrically. And decent S52s have become pretty stupidly expensive (and offer very little over an M54B30).

I mean, if I bought this (I won't - no time), I've got an old Turner World Challenge head and Schrick cams sitting around. With headers, that's good for 30-50hp at the wheels.

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2011 M3
2006 Sierra 2500HD 4WD LBZ/Allison
2004 X5 3.0i 6MT
1995 M3 S50B32
1990 325is
1989 M3 S54B32

Hers:
1989 325iX
1996 911 Turbo