nios 2 custom instruction having multiple inputs

You cant move 8 inputs to a custom instruction in a single clock. You can use the register file interface, or use multiple opcodes to break up the data from the execution.

Often, custom instructions are being used to speed things up. So if you care about performance, you need to look at where the 8 input data are coming from. If they aren't already in the register file, the NIOS would need to take some time to get them there before executing the CI. - maybe that's fine or maybe that's terrible depending on your goal.