So I think I have only option of a=clk and b=input.

Any more ideas;-(
If you only have ONE option, how can there be more ideas?

Anyhow it is mandatory that you take care of the interrupt vs main synchronization (disable int or compare). Another thing: for a= clk and b= dir do not interrupt on B, read it in the A ISR. If you do not handle the very higfh frequency 'noise' when the encoder stop across a boundary, you WILL get occasional misreads.

Erik