1) Look through your main theme files and see if there is any leftover code from apps you uninstalled. This is common because when you delete an app, Shopify immediately revokes access, so the app can't cleanup any code that it added to your theme. The main place you'll find old app code is theme.liquid and product.liquid (or it's sections / snippets).
3) In our full app analysis we also analyze slowest / heaviest loaders and look for errors, bottlenecks, and conditional loading opportunities, but for snuffing out extra files my points #1 and #2 is handle that.
Good luck on the investigation. If you find it too time consuming and want to hire an expert, feel free to reach out to speedboostr.com/contact. My team does stuff like this on a daily basis.
• Creator of Order Automator (automation app to save you and your team time on admin tasks) • Shopify developer for +10 years • Contributor on the Speed Boostr blog • Guy who likes to help people