What is the best way to organize myself to get the whole thing done?

I found the following from my old notebook, but I forgot the source of it.

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TIME
What is your realistic available time?

Understand the work entailed in a PhD
Not only do you need to know the sequence of the tasks, you need to know when you are going to do them and how long they are likely to take.

You need to plan where you will be ideally by the end of each year.

For some people, having a vision of what will happen over the next month is enough; others need to plan on a weekly or even daily basis. You have to see what works for you and don't just adopt a plan that works for someone else.

When you have settled on your plan, you need to be flexible enough to change it if it's not working.

Planning
Whatever you plan to do has to be quite specific.

Regardless of style of plan, it still is a good idea to set time limits for tasks as they can stretch and lead you in various interesting but irrelevant directions.

To avoid burnout, you need to build into your plan rest, recreation, fun, spare time and even 'catch up' time.

As with most things, planning involves trial and error. You are unlikely to get it right the first time. You need to think about what worked and what didn't work for you, modify your plan, trial it again, and continue the process.