I've done freelance work similar to that (redesigning w/ bootstrap), and I found having a set price for the completed work has worked well for me.
On tracking, I worked with a consultancy a while back and had to use self-tracking tools like toggl, and it was a dealbreaker for me. I absolutely hate tracking (billable) time, some places do it down to the minutes, it's madness IMO. It was frustrating because a problem could be solved in 2 mins, but required 1hr of research/experimentation, when do you start the timer? Oh and you have three other clients, and whenever you context switch you gotta quickly do it in the tool so it tracks the right client, etc. it warps the brain IMO and stifles creative play/thinking, especially when you're docked for not having enough billable hours, even though in a normal full-time job things would be swell. After I left, I had to readjust to not always think about my time per task and felt relief and clarity again to solve problems with an open-ended mindset.
I think devs should resist this micro tracking tools, they're used by agencies to exploit their employees and their customers—IMO it's no different than an amazon warehouse tracking their employees every move/micro-break.
Edit: Like others have mentioned here, name and shame, they scammed you! Lesson learned, but 46k is a lot of money, and for a lot of small businesses that could have been enough to tank the owners financially, so you may potentially help out others by attaching their name.