Digging up an old thread but I just finished a clutch install on my 2006 S. I wanted to add a small follow up on getting the gearbox back in the car. After fighting it on the jack for an hour, I cut a 2x4 to length to rest on the strut towers and used a ratchet strap under the trans up against the bell housing so the trans floated even with the engine and the trans slipped right in with no hassle.
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MINI Cooper Clutch Replacement (R50/R52/R53 2001-2006) | Pelican Parts DIY Maintenance Article