So not only is the US bureaucracy entirely unprepared for such a confrontation, but the US electorate just chose a failed real estate mogul turned reality TV show star to go head to head against a former Cold War operative that trained and worked for the KGB/Stasi. And go head to head they will. You can bet Putin will exploit the Trump presidency for as much as he can and there's little we can do to stop it other than voting Trump out of office next time.
I think the best analogy is the infamous wargame the US armed forces carried out in the 2000s. The blue team had an aircraft carrier and other cutting edge weaponry while red team had only basic equipment available to insurgents. The high tech weaponry worked just fine in Afghanistan but when faced against a comparable adversary (red team was led by an equally experienced general), the entire blue team was ripped to shreds by a few dozen men and some speed boats. Obviously the western intelligence apparatus is superior to Russia's but it has spent the last 20+ years focused on a completely different type of adversary. It would be like using an aircraft carrier to fight in the middle of the Himalayas.