Help in CRC custom instructions please.

I agree with your assessment, using custom instructions can be very restrictive. You will have a lot more flexibility if you design your own SOPC component with an Avalon Memory Mapped slave interface. You can have as many registers as you want and use as many cycles as you want to perform your operation.

If you have big transfers between your core and the main memory you could also implement a Memory Mapped master interface that can directly read/write to the memory but it is a bit more tricky to implement. I think the SOPC user manual as an example with a checksum hardware core that does exactly this.