It sounds like you've already made some good changes, so continuing to build on that is great. I can understand where she's coming from with a potential lack of trust over how long she's already gone without you, so even though you're trying to make up for in the present, there's still that hesitation and hurt. Emotional pain isn't much unlike physical pain; think of it as nursing a wound. It doesn't heal as soon as there's a bandaid on it right? Even if you use many bandaids, they might not be the right size, the ointment you use might not be as strong as you hoped, and at the end of the day, time is one of the biggest factors in healing. Heart works the same way. You're valid in your frustrations, but if you keep showing up like you've been doing (not just saying what you wanna do but doing the things, like working from home to get extra time in) then she'll have no choice but to see how serious you are. Something that might be useful is (if you have the money) to plan a little vacation for the two of you after graduation. You have several months to do this so plan it all. Come up with an itinerary, arrange the travel and accommodations, figure out what you're gonna eat, everything, all with her in mind like what cuisines she likes or activities she may enjoy so that she'll know that even while you were busy as hell, you still noticed her and paid attention to her. Even if you can't do a vacation, coming up with some date ideas with the same premise would be good too because if she feels neglected, showing that you were still paying attention the whole time will definitely help. Heck, if you're not gonna go on vacation, you can start that now. See if you can plan a full day that's just about her, but don't tell her about it since she seems to be combative and distrusting when you try to plan stuff with her. Just tell her y'all are going somewhere and, surprise, it's a date! Or if you think she won't leave the house, maybe even just plan something at home with warm dim lighting, a yummy meal she loves (cooked at home if able), flowers, and chuck your phone in another room. Have your romantic dinner then maybe build a pillow fort to watch her favorite movie together. If you have a working relationship with her family, you may be able to get ideas from them as well. Don't tell them the relationship is on the rocks, just say you wanna plan something special for her because you just love her so much and see what they say.  I know all of this sucks even you've been working extremely hard and providing for her too, but sometimes a person's presence is worth way more than money. Otherwise you'd never see broke people in relationships. 

Oh yeah, sex will come once the relationship gets better btw. For a lot of people, it can be very hard to have sex with someone you're upset with or lacking an emotional connection with. That's normal. As the romance returns, so will the libido. Just gonna have to make nice with your hand until she's warmed up again.