Welcome to the Q&A Forum

I recently did something similar and left behind a bunch of "thin" pages, just be sure to check your internal links to make sure you are not linking to a page you are 404ing. [Screaming Frog is great for this—if you don't have it, you should get it.] You can always "revive" any that you see a lot of people trying to reach. My redirects took hold quickly—I couldn't even say how long, it was that fast. [Mine was an old domain and frequently crawled.] Good luck!

Can you clarify what you're concerned about for 301 redirects in terms of link juice? 301 redirects don't carry as much link juice as a direct link, but it doesn't impact correct links, just the links that, otherwise, wouldn't get link juice to your end destination at all. (Though, if your canonical is working correctly, it'll pass the same amount of link juice as a 301 redirect.) Dr. Pete goes into this a bit more over here: https://moz.com/community/q/do-canonical-tags-pass-all-of-the-link-juice-onto-the-url-they-point-to

Website Grader just analyzes the presence of specific tags and sections.  It doesn't analyze the overall quality and effectiveness of the page. Meaning, I can get an "A" and make a page not rank very easily, as well as being able to get a page to rank decently while still getting an "F."  It all depends on how competitive the vertical is, and how authoritative my domain is.