the flue should not allow water in!
it should have a slight tilt so water does not flow into your boiler and rot it! hence your fan change etc.
The solution here would be to get the inital problem fixed with the flue before addressing anything else.
On that note, all new condensing boiler SHOULD have the flue inclined to allow water & condensate to flow through the boiler, but these are made of stainless and won't rot like yours will
T
April 2008