Check the condition of the rear hatch drains (R50 and R53), when I did a detailing on my '05 MCS recently, I found the drains (2 small rectangular holes at the bottom seam) were packed up with black, greasy glop. They weren't so bad that nothing could drain, but enough to to limit the amount and allow for water to puddle and possibly start corrosion at the hatch seam.
A little fettling with a small flat blade screwdriver opened them up again.
Just a heads-up that could save your hatch down the line.

 

Thanks for the info. Good job.

 

String trimmer line is excellent for clearing drains. Strong enough to clear the clog without doing any damage to any subsurface plumbing.

 

Good mention , those other drains, the big ones are the drain tubes on top also.

https://www.northamericanmotoring.co...-problems.html

 

Good find. Those drains getting clogged is somewhat common and can cause a whole hoist of water leak issues with your MINI.

 

I'm at a loss - where are these small rectangular holes? In the hatch? In the body?
I see the two at the top of the body, but that's it.

 

They are in the hatch itself. If you open the hatch and look at the area of the hatch near the catch, they are about 12" each side of the catch right at the metal seam of the hatch.
HTH,

 

Huh - my late '03 build '04 only has one right at the latch D ring. TFTH.

 

Its the little small holes in the hatch itself at the bottom of the seam to let water out , usually filled with a little grim an old wax coating from transposrt.