Are you are using #BS803-029 and #BS803-030 ?
Honestly my heat sink doesn't sit flush with my motor either and the only way I could get get it to fit right was with the fan not level ;if you face the front bumper my fan is tilted to the left and I have had had it like this for a while and have had no issues.
You can install it with the fan level but you have to do some modifications;some cutting but not the heat sink.