Since you have done some research on the subject, I probably can not tell you anything you have not read previously. But, just in case.
First off, the bike is new, with some sort of break in oil. The Sprint g'box is not the smoothest you will come across when new, but they do get smoother after about 4/5k miles. You can expect a noticeable improvement after the first oil change.
Every bike I have ever ridden has the first gear clunk due to the design of the engagement dogs. Some do it worse than others, but the Sprint is not the worse example.
The false upshifts are usually related to technique or choice of footware. It sounds as though you are experienced so maybe this is indeed something that you need to mention to your dealer. But, the fact that the upshifts are better with preloading makes me think that it might not be mechanical.
The excessive downshift force just makes me think that this also is related to the newness of the bike and the type of oil in it presently.
The noise you hear with the clutch pulled in is the pull rod and bearing. Usually those do not start being evident until the miles are accumulated. I do not see it as a problem unless it is more than "some noise". I suspect most Sprints do it and the owners have not noticed it. But, it would not hurt to also mention that to the dealer so that there is a record.
On a side note, the clutch pressure plate has five equaly spaced mount holes. During manufacturing, there are acceptable tolerances for each part. Sometimes (rarely) an accumulation of tolerances from several parts can occur. What this means is that any two parts that attach to each other in more than one orientation has one ideal position. The plate can be installed in one of five positions to provide the best alignment for the pull rod and bearing.
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