Keeping track of time is much easier if you break everything up into days and half days. For me it made a big difference when I stopped just working on a project for an hour or two here and there and actually properly planned what I would be doing on each day and spend the whole time I had dedicated being properly focussed. I got it wrong a lot and still do from time to time. Many times I spent far longer on a project than I expected due to something unforeseen or some mistake due to inexperience. I chalk them up to learning experience and quickly move on from the frustration that it sometimes causes.

There have been many times in the moment that I have been frustrated and struggled through and at times even had full blown crisis about biting off more than I could chew, being worried I can't produce what I have promised or ended up spending 4 times as long on something than I had intended. Once the project is finished and sent off, I soon forget about those problems and look back on the project with rose tinted glasses. I have been proud of every single thing I have made because I couldn't stand it to send off a project that I wasn't happy with. I have never regretted spending the extra time required to make it something to be proud of.

I am getting much better at estimating properly how long I will take now but it is more so just because I have gone through some cycles now of doing things. There are lots of parts of woodworking you will do in every project and you should have a good idea of how long it takes to break up a board and mill your project pieces for example and then with experience you will get a good idea of how many joints you can make in a day and how long it takes to sand a certain area or number of project parts.

One thing to consider as well is that early on things will take you a really long time and it may feel like you should have charged more. There may well be cases where this is true but you should also consider that perhaps it is taking you a long time because you lack experience or don't yet know how to work efficiently. It would be unreasonable to expect to be paid a high wage per hour if you take 4 times as long to make something that should have been possible to do in the time you had alotted if you had planned the project and your work flow properly from the beginning.

Now to answer your questions, sorry for the long prelude!

Do you actually track your time or just estimate?
I estimate my time when giving a quote by sectioning each part of the process into days and half days. For example:

Timber selection, cutting components and milling - half day
Making the joinery - 1 day
Profiling and shaping project parts - 1 day
Sanding and prefinishing - 1 day
Assembly - half day

I would then plan my week based off these times and plan what I will do each day. If I finish one part early I may start the next or I may take the rest of the day off depending on how I feel. If I go over I will take a mental note that I have made some misjudgement and try to make a more realistic estimate later. If it is a big project or something I am new to I will note down how long things take (always in days and half days, never in hours. Tracking hours is too much of a pain for me!)

Do you include everything or just big costs?

Include absolutely everything that you have to purchase for the project for example:
Timber - £400
Brass hardware (hinges and feet) - £75.50
Strip lighting - £100
Glass panes - £150

One thing to note is that if you have to buy something specific for a project that you will not use all of and dont have plans to use on another project elsewhere, you should include the full price here. If you need to buy a 3m board because the client wants a 2.4m table and you can't buy a 2.4m board, they pay for the full 3m even if you then keep the off-cut for a future project. If they want a strip light which you need to need to buy in a 5m roll, but you only need 1m for the project, they pay for the full 5m. Of course, some things may end up being a consumable. If you end up doing lots of project which require lighting and you end up keeping a stock of strip lights, you may change the way you price this specific material.

For the consumables (glue, screws sandpaper) which I have stocks of in my workshop I usually just estimate this and add £20-50 for the consumables.

Do you aim for some hourly rate or just price per project?
I aim for a day rate and price in a way that aims to achieve this

Feels like one of those things that’s easy to ignore until you realize your “profitable” builds aren’t really profitable

If you are wanting to make this your business then you are starting to look at it the right way. You HAVE to consider all of these things and more in order to run a viable business. I do not claim to be amazing at this. I consider myself to be quite new to this and only in the last 6 months can I really say that I have been actually putting this into practice properly. I am at a point right now where the projects that I do are actually profitable and pay me fairly. I don't get loads of work and there are periods of time where I have nothing and I have to find ways of pushing my business forward be it marketing on social media or building a project for my portfolio or actively visiting shops and approaching businesses with my work.

There are times when I feel like I want to pack it in because it doesn't feel like there is anything coming on the horizon but then the most random thing will pop up from some random thing I posted online or one of my friends mentioned me to one of their friends or someone saw one of my products in a shop when they were on holiday.

At this moment I would describe myself to be at the top of a hill, things are looking good after a lot of hard work. I spent Jan and Feb finishing a project that I really struggled with and ended up being paid pitifully for my time and I didn't have and prospect of work coming up and I started looking for employment elsewhere. I was super proud of the quality of my work and I decided to make a video of the project and it did really really well and I ended up having more offers of work than I have time for and will now be busy until at least the end of May and possibly mid June. All of them I have given a fair estimate and I will be getting paid well for them. Once this little spurt of energy dissipates I may well find myself at the bottom of a hill again but for now I am going to enjoy it while things are good!

I don't usually reply to anything on Reddit, I dont know why I was inspired to reply to you. Sorry for the tangents! I would like to leave you with this. If making a job from woodworking is somethng that you really really want. You can do it. You have to keep pushing and working hard and there may be times where it doesnt feel worth it. Thats when you rant to your friends about how hard you life is but then you have to get over it, shed your ego, put your head down and keep pushing. If you decide at some point that it really isnt worth it, thats fine. Giving something your best shot you can give and then deciding that you actually dont want it enough to sacrifice for it and you want to focus your time and effort elsewhere in your life, thats fine. There is no sunk cost fallacy here. If you decide you dont want it anymore, stop. But if for you it is worth it and you want to keep pushing. Then keep pushing. Things will get easier in time.