The reason you are getting the vibration is, the engine should idle at around 800rpm. Down at 500rpm vibration will be a lot more pronounced. You shouldn't get any vibration up at 1000+rpm. I've read reports on other sites people feel it clears up around there. Even at 800rpm there will be a slight vibration.
I'm thinking you already had a vacuum leak at the intake before it popped off, which allowed your idle level to drop drastically after you did your fix. Due to this, you need to probably do an idle relearn, plus clean the IAC and MAP sensor. Here are some procedures from what I've learned today (from this site):
- Unplugged battery
- Disconnected the map sensor
- Whacked on the plug outlet to clear out any debris
- Sprayed with compressed air to clean out any debris
- Plugged back sensor
- Ensured there was a good connection
- Zip tied it around the plug horizontally and vertically
Unplugged the sensor
Tilted over the IAC to get a good view
Sprayed carb cleaned into the IAC liberally (unfortunately I was not able to get out all of the black build up) the canal on the side looked cleaned but in the middle chamber there was still some black markings along the side walls, I was afraid of using a Q-tip or brush because it might of left some bristles in there causing more troubles reinstalled IAC with a thin layer of oil reconnected the sensor
Reconnected the battery
Let it idle for about 15 minutes
Took it for a drive and NEVER COASTED only downshifted through all the gears until 2nd where I preceded to wait till 1k before I clutched in and braked completely.
Mind you, this was copied directly from the forum, the advice appears sound.