Hi,
You can refer to following post:
https://community.freescale.com/docs/DOC-102559
This demo example does the same you have except of DMA is used to read the CTU FIFO finally.
But you can use the FIFO overflow interrupt instead of DMA if needed. This is also mentioned in the document in fact.
In your case do not use Trigger 1 interrupt but use FIFO0 interrupt (vector 202) and set CTU FIFO registers properly, means set FIFO threshold and enable overflow interrupt.
BR,
Petr