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Communication is the key. For example, I'm trying to figure out from your post what the actual problem is. It seems like you don't know, which is not exactly a surprise. You say "I think she resents my being in her space during weekdays." First of all, you can ask her what the problem is. Second of all, you can try to give some breathing room by working in a coffee shop or something.

Of course that one issue is not everything, but it is something that could be worked on in the short term.

I highly recommend the book Getting the Love You Want.

edit: Rereading this, it sounds more brusque than I intended. Also, if you do ask your wife what is wrong, that can obviously be a charged conversation. Getting the Love You Want has a technique called the imago dialogue. Even if your wife (who seems reluctant to therapy) won't engage in this, you can still use the techniques yourself. For this particular conversation you want to focus on mirroring, that is: let her speak, then repeat what she told you and ask if you summarized it correctly. If you're not both on the same page, this may end up being one-sided. The point is to make sure you understand her point before you make yours (or vice versa). You will often see you're upset about very different things.

The book is really fascinating.