Hi jah,
You cumulative GPA is a bit low but the 3.8 in the later years is a pretty solid performance and make sure that you point it our either in your CV or SOP by explaining how you were able to learn from the first two years and made such a significant improvement.
In terms of applying for top-tier school, I'd say study super hard for GRE and aiming for 800Q and 700+V to get the attention for the admission committee.
Your experience and LORs sound pretty solid to me and make sure that you address your experience and patent application very well i yout SOP!
If you want to boost your chance, I'd suggest check out a new startup founded by Stanford grads that provides online platform that connects current top-tier school students with applicants to help them get into their dream schools (which sounds like your case a lot). I've been their alpha tester and think it was very helpful. They are launching their beta test in early May so definitely take advantage of that!