This is a very curious problem. If he does not create the Confederation of the Rhine, but keeps meddling in Germany (marshals in Cleves, Auerstadt, whatnot), then I don't think it will make a penny worth of difference. If, on the other hand, except for the Bavarian alliance, he stops intervening in Germany, he will have slowed down the growth of German nationalism.
No, he wouldn't have. Its not like all those countries weren't part of a "Germany" (a weak one sure, but a germany none the less) before. Once he puts a whippin on austria he discredits there ability to protect Germany; Which although was a fact for awhile, people were fine with that as long as they at least pretended to.
As soon as the Austrian's give up the imperial title they dissolve Germany and all of those mini-states start looking for a new Germany or at least a new protector (which came in the form of Napoleon I, and then as soon as he was defeated Prussia.)
I think people over credit Nappy as if Germans didn't want a country before. The truth is they had one before him, he created a new one and when he lost they immediately started trying to reunify.
To answer the OP: He either created something very similar, or isn't the same Napoleon as OTL and didn't dissolve Germany in which case the HRE remains until Prussia industrializes faster than Austria (which is very likely considering things like minorities, ultra-conservatives (Prussia basically lost ultra-conservatives for awhile because of Napoleon defeating them), ect.) in which case we probably still see an Austro-Prussian war.