LVDS clock signal EMI
Are you working with an OTS board or do you have control over the i.MX53 Board?
If you can change the board, you could have a look at the following:


Correct (differential) trace impedance
Good layout: ground or power layers next to every signal layer
very good decoupling of i.MX and fast switching components
do use twisted LVDS pairs
use a suitable connector for high speed signals
correct pinout on the connectors


In all cases, even if you can't influence any of the above: look into drive speed and drive strength of the i.MX ports. It might or might not be available, but reduce as far as possible.