Srob70 - You say you're mainly happy, love your wife, want to spend as much time together as possible. You were both independent and self-sufficient; you both chose to make a life together. It sounds to me like (1) there's some confusion re what you each need from the relationship now and (2) you're (both) having some trouble communicating openly without arguing, accusing, and getting angry/giving up.
I think you need a long, calm, honest conversation about each of your needs and how they can be met within the relationship and within the living arrangements. The kind of talk where each person can say anything, and the other person listens and hears and thinks and then responds. Don't wait for an argument or disagreement to talk about all this - make a time and do it proactively. If those kind of talks keep veering off into accusations/anger, perhaps a relationship counselor could help (would probably have to be online/video call, etc. for now)?
A few specific things -
Is living together in her house the long-term plan? If you moved into a new place together, you'd compromise on which items from each of your houses got used versus stored vs sold/donated, but in this case it sounds like you're in her "space" and must make do with what's there. I personally wouldn't like the comments about how she's given you her house - have you told her how you feel about giving up your place?
Is she alone all day when you're out at work, and is that the norm for her or is it perhaps because of COVID? If she's used to being out and about and that's changed, she may be starved for company. And you're out in the world most days, probably dealing with people all day at work, and need some of the down time and alone time she's already had all week. There may be personality differences at play, too - some people need more closeness and want their loved ones close-by even if they're not doing anything specific together; others genuinely need more "space".
Could it help to have a bit of a plan ahead of time of how the evenings and weekends will go - for example, mention on Friday that you'll need to spend most of Saturday day working outdoors, but also plan a dinner and evening together? You could even plan to cook dinner together. Do you need to go on walks alone (it's understandable if you do), or could you sometimes go on walks together? Can you encourage any interests or hobbies she's had, that she may have put on the back burner recently? Just suggestions; you get the idea.
Finally, re the cup in sink incident. I used to be a scream-and-throw-things type (only very occasionally, when very angry) and considered it trivial - after all, I wasn't throwing things AT anyone or causing damage. But a lot of people are bothered by this kind of behaviour and may even experience it as aggression or violence. What seems unremarkable to you may be startling and worrying to her, especially if she has any history of abuse or trauma.
Again, I'd just talk calmly with her about it - see what she says, and if it is causing her distress, try to avoid that for her sake. She should do the same if there are "innocent" things she does that drive you bonkers as well - but she'll only know if you stay calm and open enough for her to tell you and for you to understand, and vice versa.