While not a native PDF, the famous "Kanji Damage" or "Core 10k Anki" decks can be exported to CSV and then printed as a PDF. Use the add-on "Export as PDF" in Anki to create a personalized 5000-kanji document.
Look for PDFs specifically labeled for Kanken (漢字検定) . Sites like Scribd often host community-uploaded reference guides for these higher levels. 5000 kanji pdf