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When I drained mine I removed the left side fairing and pulled the hose from radiator to the water pump at the water pump on that side (I believe it went into the water pump). Not sure if this is proper protocol but I never had any problems. Just reattach snuggly.
 

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Here are instructions for a 06 1000 from the manual.



ENGINE COOLANT CHANGE
• Remove the under cowlings. (8-5)
• Remove the radiator cap .
• Drain engine coolant by disconnecting the radiator hose 
from the pump.

• Flush the radiator with fresh water if necessary.
• Connect the radiator hose  securely.
• Pour the specified engine coolant up to the radiator inlet.
Engine coolant capacity (excluding reservoir):
2 150 ml (2.3/1.9 US/lmp qt)
• Bleed the air from the engine coolant circuit in the following
procedure. (2-18)

ENGINE COOLANT INFORMATION (7-2)
Inspect every 6 000 km (4 000 miles, 12 months).
Replace engine coolant every 2 years.
* Do not open the radiator cap when the engine is hot,
as you may be injured by escaping hot liquid or
vapor.
* Engine coolant may be harmful if swallowed or if it
comes in contact with skin or eyes. If engine coolant
gets into the eyes or in contact with the skin, flush
thoroughly with plenty of water. If swallowed, induce
vomiting and call physician immediately!

2-18 PERIODIC MAINTENANCE

AIR BLEEDING THE COOLING CIRCUIT
• Add engine coolant up to the radiator inlet.
• Support the motorcycle upright.
• Slowly swing the motorcycle, right and left, to bleed the air
trapped in the cooling circuit.
• Add engine coolant up to the radiator inlet.
• Start up the engine and bleed air from the radiator inlet completely.
• Add engine coolant up to the radiator inlet.
• Repeat the above procedure until no air bleeds from the radiator
inlet.
• Loosen the air bleeding bolt  and check that the engine
coolant flows out.
Air bleeder bolt: 6.0 N·m (0.6 kgf-m, 4.5 lb-ft)
• Close the radiator cap securely.
• After warming up and cooling down the engine several times,
add the engine coolant up to the full level of the reservoir.

Engine coolant capacity:
Engine side : 2 150 ml (2.3/1.9 US/Imp qt)
Reservoir tank side : 250 ml (0.3/0.2 US/lmp qt)
 
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