I'd have to see a pic to be sure, but basically the PCV should have the valve itself in one cover, with a roughly 3/8" tube going to a matching fitting in the base of the carb. Different carbs have them in different positions though. Some in the rear, some in the front, some in the sides. I worked on a 'Cruiser with the fitting on the passenger side base, so I put the valve in the passenger side valve cover for convenience.
Then the other valve cover would get the simple hose fitting to run a tube into the air filter housing somewhere. That, or there would just be a cap with it's own filter put there if that was easier. Just as long as it's filtered air being pulled into the cover opposite the PCV valve, you should be fine.
Your high idle could simply be adjustments. Everything has to be balanced, from the ignition timing, to the throttle blade and choke mechanisms, to any electric throttle solenoids. Include in that mix any air leaks, and you've got a system.
Lots of potential vacuum leaks in a new system too, so when you get it idling somewhere closer to 1000 rpm, start spraying some carb cleaner, or even water, all around the place to see if there is any change in the idle speed/quality when you hit a certain point.
Paul