The answers, before you have to ask.

Upload the archive through Extensions → Installer, then open Extensions → Modifications and press Refresh so OpenCart applies Nitro's patches. Then install Nitro from the module list under Extensions → Extensions → Modules. That install step does the rest itself: it applies the Recommended profile — which turns the master switch and the full-page cache on — writes Nitro's runtime settings file, registers its OpenCart event hooks and adds one guarded line to your storefront index.php. The engine is running by the time Install finishes; opening the settings page afterwards is for tuning, not for starting it.

Yes — do it straight after uploading. Several of Nitro's fastest paths are ocmod patches rather than event hooks: the query-cache delegate in system/library/db.php, the replacement file-cache internals, the fast image resize, the storefront template engine, and the hook that makes Journal3's own Clear Cache button clear Nitro's cache too. If you skip it, Nitro still installs and the page cache still works, but the Diagnostics tab's Query delegate (db.php ocmod) row will tell you to go and press Refresh. Doing it later is fine — no reinstall needed.

Only for the work that runs on a schedule — the storefront serves cached pages without it. The Cron tab prints the exact command with your server's PHP CLI binary already detected, and recommends running it every five minutes. One entry covers all of it: crawling the store as a guest so pages are pre-rendered before visitors arrive, deleting expired entries, trimming the cache to your size cap, recording product views that the cached serve path cannot count, picking up products edited outside OpenCart, and rebuilding the price index if you use it. It refuses to run over HTTP, so there is no token to protect and no request timeout to hit.

Upload the new archive through Extensions → Installer and press Refresh under Extensions → Modifications again. Do not uninstall first — your settings live in OpenCart's own settings table and are left alone. Nitro notices that its runtime settings file no longer matches what the admin has saved and rewrites it by itself the next time you load any admin page; there is a Re-apply Settings button if you want to force it. A release that adds a new option leaves that option off until you turn it on, so it is worth reading the release notes and looking over the settings page afterwards.

Uninstall the module from Extensions → Extensions → Modules. That removes its permissions and event hooks, takes its one line back out of your storefront index.php, deletes its settings, drops the price-index table, and deletes its storage and cache directories along with every generated .nitro.css, .nitro.js and bundle it wrote beside your theme. Then remove Nitro under Extensions → Modifications and press Refresh so the ocmod patches come off your core files. Three things stay on purpose: the extension's own files until you delete them, the .webp copies in image/cache, and anything you applied from the Database tab — added indexes and InnoDB or utf8mb4 conversions are not reversed.