Cyclone III pin assignments problem

usually Qsys systems are generated for spécific reasons (compatible with what they are driving).

taht means every component's existance is justified and removing one may cause a failure.

since you are using a tutorial provided by Bitec, you should wether understand the purpose of every coponent and how do they communicate and work the alter it,

or stick with the given Qsys system and add what ever you need for your project because adding component won't harm it.