I hear that the funduro's have a much better reputation for reliability then the new f650's.
If it is not too late for you to change bikes I would say go with a KLR. It will be much easier to find parts and will break less on you. Just make sure to find an old one with low miles. There is no sense in taking a high mileage bike on a trip like this because you will run into replacement problems.
I did this trip with a 2001 BMW F650 and know all about the rip off BMW parts prices down there. Expect to pay $40 for an air filter and $60 for aftermarket brake pads.
Also, breaking down in the middle of no where and having to have your bike towed 400 miles to the nearest mechanic is always fun.
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