I agree with @Eva’s wise comments above. Well done, I am proud of you.
Excellent idea, and it should work well.
If it is single comb (not two pieces hanging side-by side but welded together), I would trim it back until it fits. A bread knife or an uncapping knife is best for that kind of thing. If it truly is that deep on each side, it won’t have brood in it, just honey. You could save the trimmings and crush and strain them through an old kitchen sieve or colander.
If it turned out to be two combs, I would separate them completely and rubber band them into the frames, or push them onto the wires as you did you before.
You could rest it on top of the inner cover, under the roof, leaving the hole in the inner cover open for now. That is usually perceived as outside the hive by the bees, and they will take it down over a day or two. Keeping it inside the hive prevents the risk of robbing that @Eva mentioned. If it is too thick to fit under the roof, you could put an empty deep box above the inner cover, and put the frame in that. Remove it after a couple of days, or they may start to build under the roof though. I know my bees would!
- The color difference will be because the bottom box was used more heavily for brood last season. When brood develops in comb, it leaves some shellac behind on the wax, which is very dark and quite strong. Comb only used for honey stays much lighter.
- The cross-combing difference may be because you managed the bottom box much more actively, then took a more hands-off approach with the top box. You can never trust bees, and if left unsupervised, they almost always get creative in the most unhelpful ways!
Anyhow, I think you did well, and perhaps learned a lot too.