I have a '82 GL1100I and I've read in forums that a similar problem with noise occurs at low RPM could be the primary chain which has a little stretch therefore is slapping the case. I believe that's the reason why my clunking noise is happening? At least this sounds little less of a problem than a slipped bearing. My sound goes away as soon as I get about 2k RPM.
That's usually precisely what it is - that primary chain slap. I've never heard of them stretching or getting loose, but what DOES usually cause that noise is uneven power pulses coming from the cylinders. Basically, meaning the cylinders are not generating the same amount of power, which sets up a vibration in the chain, which makes that noise.
Normally this can be fixed by re-syncronizing the carbs, which balances the cylinders' power output, and smooths out the pulses. However in a fuel-injected bike, there are no carbs.
You might want to check the compression of your cylinders and see if one or more cylinders is down on compression, which could explain the uneven pulses causing the chain noise.