You raise several issues here:

The problem with reserve in this case is most likely either the upended U bend or the fact that the bottom of the tank is too low for fuel to flow into the carb voluntarily. I have similar problems, but only when the fuel level is low. I take it you have problems even with a full tank?

There is no vacuum pump, there is a vacuum operated fuel tap on the stock tank. When the engine stops there is no vacuum and the tap closes via a spring-loaded membrane.

The clunk: have you checked your bike for the "engine grenade" problem? See separate topic on this deadly issue. If your bike is first registered in 99 then it may be a 98 model and they are ALL concerned, as far as I know.

Interestingly, my former gf's DR had a lound clunk when starting or stopping the engine. The noise sounds horrendous, as if the engine was about to explode, especially if the bike doesn't want to start. Mine didn't have this problem and neither bike has the engine grenade parts. Through a process of elimination I have narrowed the cause down to the starter clutch. I can't see anything wrong with it, but hers lets go a little before engaging when you turn it by hand. The proof came when I swapped it into my bike: I now have the noise and she doesn't. My bike now has well over 140000 km on the clock and the starter clutch has done even more. It still makes this noise every other time I stop the engine. I'm no longer worried about it. (Famous last words... )

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Cheers,
Peter.

Europe to NZ 2006-10