So far I've been using Simple Time Tracker, which is just a random open source app I found on fdroid that lets you input the name of a project and When you had go, it tracks your time.

Tracking is good not only for the client, you can be as transparent or opaque as you like, but so that you know how much time you actually spend on a project. Overtime you will be able to set simple standard fees for basic elements because you have a genuine idea of how long it takes you and you can bake in your profit. Look into LEAN practices and see if it helps business mangement for you.

I’m terrible for this and I nearly always overwork for the benefit of the client. I have this fear that I’m slow and therefore don’t account for all the time.

Also, sometimes time means wandering around or relaxing to get an idea. It feels difficult charging for that time but it’s necessary.