That's pretty standard procedure for a Nissan dealership to follow. After all, they can't be certain all your aftermarket equipment was installed properly or the quality of the parts themselves. Even a pinhole casting error on the headers, or a misaligned intake can cause leaks that would affect idle. It's why using aftermarket mods is a double edged sword.
One question: why do you need a stage I clutch? It won't really add to the performance or durability of the Z. If your flywheel is in good shape, why not check into the costs of a Nissan Value pack clutch kit. They combine all the parts needed (except a flywheel) at a discount from buying them separately. At least it'd give you a comparison price-wise.