Just a thought: You said she was much better at paying bills which (I assume?) means she's got a better financial head than you. Some people may earn more than their partner, but that doesn't necessarily mean they're better at spending, investing, etc.
I think 1 of 2 things is going on:
1. She doesn't like HOW you're spending "your" money.
First of all, I don't think that this is your money. It sounds like you combine everything else so as a wife I'd find it pretty strange if you were suddenly territorial over extra cash. If you always had separate finances (or some separate finances) it wouldn't concern me, but I find your desire to keep this all to yourself... Curious. I wonder if she does, too? Can you really blame her for not being happy under this circumstance?
Second of all, what exactly are you spending this extra money on? Tool? Booze? Food? Toys? There's a possibility she just thinks there's a smarter/better way for you to be spending it. Maybe she doesn't even want it for herself, but she'd rather you spend it in some more "productive" way. I'm not saying her way is the right way, but maybe she sees this extra 4k/year as vacation money... Or financing a new car, etc. My husband could spend money on dinners, clothes, toys, etc. whereas I'd rather upgrade the car or go to Europe. Have you considered trading off who gets to make the final decision as to how that money is spent each year? This could be a glorious compromise. Every other year we switch off on our tax return and money from his side job! (He does roofing, builds decks, etc.) Whose ever turn it is gets the final vote as to what it's spend on. Last year my husband bought a snowblower (we don't even have a driveway as of yet... It's a shared lot we don't even shovel, lol), but this year it's my turn and we're going to Paris.
I think you should ask her how she'd like it spent, just to see where her head is at and if you can come to a compromise.
2. She feels lazy, inferior and not as ambitious in comparison.
It doesn't sound like you spend too much time on these side jobs so I don't think it's an issue of not spending enough time together. (Unless you're choosing to work on your anniversary, lol.)
I admit, my husband's side jobs can make me feel lazy. He doesn't do if often, same style as you, but it makes me WANT to contribute more. I feel like if he's going to be spending Saturdays working I should, too. He just re did my mother's entire basement and I just sat there thinking I wish I could help. (I tired to hammer one floorboard in and cracked it so was immediately whisked away, lol.) I talked to my husband about this and he told me if I want to get a side job for myself he'd support it. It hasn't happened yet, but when we buy our home in the next year or so, we've agreed that I'm to have an entire room devoted to a small business. Nothing crazy, but I'd like to sell products I personally believe in/use (Scentsy, Cruelty-Free products - especially cleaning products... Those are littered with animal testing) hair extensions, etc. I'm also a certified Nail Technician so I'd like to do nails on the side at my convenience. I do my own nails weekly so having a space devoted to this isn't even wasteful if I don't bank a lot of money.) The idea of it has made me feel more equal. More worthy. Maybe it's silly, but I just wanted to contribute.
That's just my input! Update us. Hope everything works out,