Firstly...

Welcome to XT660.com

You should be fine with a later pump. The part numbers are the same for all models (5VK-13907-01). In 2009 the last two digits changed to -02, but this only signifies that is an updated/improved version of the same part.

Not sure about the one in the link, doesn't look right to me?

As for cleaning the rust out of your tank, there is a DIY method that costs very little and has worked well for me in the past (although I've only ever done it on bikes with fuel taps which have smaller holes to plug.)

Take out the tank and take off all the fittings, pipe work etc. Seal all the holes (except the filler). Tip in about 500g of brass tacks and about half a litre of diesel. (You can use almost anything - nuts, bolts, screws, some even use sand, just bear in mind you need to get it all out at the end! Brass is good because it's softer than steel, but harder than iron oxide.) Seal the filler hole. Shake/swill in as many directions as you can for as long as you arms can take - the longer the better. Pour out the diesel/tacks and flush with petrol. Repeat if necessary.

To prevent the rust coming back at the top of the tank, always try and keep the tank full particularly during the winter months and in storage. Use a fuel stabliser too for long periods when not in use.

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