The trick is to work your own motivation into your workflow "I'll get a coffee when I finish my emails". "When I finish writing this draft, I'll get a beer". "I'm going to slog through this, and then take myself out to dinner". Whatever tickles your fancy.
As for the to-do list: keep it simple. Using a fancy app tempts you to waste time beautifying the list, with categories, priorities, and other unhelpful nonsense. That doesn't get anything done. Personally, I use a simple text document. It auto-opens when I log in. The stuff that needs done first is at the top. Stuff to do "when I have time" accumulates at the bottom. Every few months, I delete stuff that is no longer relevent; otherwise the bottom part would grow forever.
Finally, a last trick, which comes from my wife's PhD advisor. Always end the day with one little, easy task undone. The next day, tackling that easy task helps get you back into a productive mindset. Try it - it really does help!