re: I can accept that Putin wanted Trump to win, but

There are two valid reasons why Putin would prefer Trump to Clinton:

1) Oil - the Russians control the flow of natural gas into Europe through their partnership with the Iranians. This is not good for business for the Gulf States, primarily Saudi Arabia. There is a reason why the Clinton Foundation was accepting millions of dollars from the Gulf States themselves and their proxies. There was an expectation that the Clintons would use their power and influence to derail the flow of Iranian petrol to Europe through Russia.

2) Russia's Civil Wars - The Russians have been fighting wars with Chechen and Dagestani Muslims for decades. These hot zones are in the Caucasus region not far from the violence in Turkey and Syria. The Russians want groups like ISIL contained less the violence spill over into the Caucasus. They know Clinton is nothing more than a neoconservative and is far more likely to meddle and engage in war in the region, especially to depose Assad. Trump actually presents as the better choice because he has tended to be more of a non-interventionist given his opposition to the Iraq War.