I had the same problem recently. Could be your carbs out of sync or an air leak at the intake manifolds.
Start it up and spray some WD-40 around the entire joint of the carb boot to the head, and the carb boot to the carb, on both sides. If your idle surges, you have an air leak.
If not, that points to carbs. You will need a manometer and the carb sync tool to accurately sync the carbs. I use this kit and it works quite well
http://www.common-motor.com/honda-360-carburetor-synchronization
You can also pull the carbs off and "bench sync" them. The sync screw is between the two carbs. It has a flathead slotted head on it, with an 8mm (i think) nut on it. This screw controls the difference between how open your throttle plates are at 'closed' position. To bench sync, open the idle speed screw (big screw on the side with ridges for your fingers) until you can get a straightened paperclip slid underneath the throttle plate on one side. Then, use sync screw to make them match. The sync screw only changes one side, so make note of which side that is, and do the other one first. The paperclip should feel exactly the same coming in and out of underneath the plates. It should just barely drag, so as not to damage the plates or carb body. When they are close as you can get them, back the idle speed screw all the way out so the plates are just about closed. There is a stop screw that moves when you twist the idle speed screw, make sure it is just barely touching and not opening the throttle plates at all. Put the carbs back on, and it
should idle better. Clear as mud?
A lot of shops don't know what the hell they are doing when it comes to older motorcycles, so beware. The 360 should idle at 1200 RPM. You shouldn't be riding it when its idling at 3-4k.