Do I need to replace the header studs or can I reuse the old ones?

Reuse your existing studs if they're in good shape—no corrosion or thread damage. If they're bent, stripped, or corroded, swap them out before installing the new gasket. Torque to spec when you reassemble.

Should I clean the header and cylinder head surfaces before installing this?

Yes. Scrape off all old gasket material and carbon buildup from both surfaces with a gasket scraper or wire brush. Wipe clean with a rag. A clean, flat surface is what keeps this seal from weeping.

Will this work with a stock header or only aftermarket ones?

Works with both. This gasket is designed for the factory mounting points and bolt pattern on the 4.6L head, so it seals regardless of whether your header is OEM or an aftermarket bolt-on.