Noise is likely nothing..mine make a slight clunk noise from the u-joint if the wheels are lifted off the ground as I spin them.
The engine mount thing I've never seen before..suggest you loosen off all the bolts and shake the engine to be sure it's settled into place. The top mount only goes in one way because of it's shape..
Post up some pics..maybe a video of the noise.
Lets have a look..
Current toys..
1986 Honda 350X..trail bomb!
1985 Honda 250SX..my main mudder
1985 Honda 250ES..Back in Black Trike
Current non-trike toys:
1990 Honda TRX300FW
1995 Seadoo GTX
1998 Polaris Indy Lite 340(Nearly new looking)
1998 Polaris Touring 500
1998 Club Car (electric)