My suggestion for Tokyo:-
1. Uniglo heattech long sleeve T for first layer (the normal one should do, get the warmer thicker only if going to places temperature going minus).
2. A normal slightly thicker cotton long sleeve T for second layer (wool or fleece T if you really can't take cold one, but plus point is wool or fleece may suffice sometimes so you may not need the outer layer if temperature not that cold).
3. For bottom, get the uniglo pants with fleece inside as suggested by someone. Else, thicker jeans also ok but you might feel cold when wind blow (you may standby Uniglo heattech pants wear inside if needed)
4. For outer layer, get a light WINDPROOF jacket if you can (some comes with fleece inside, some without which is fine if your second layer already wear fleece). There is no need for Heavy Down (inconvenient if you need to remove it when inside buildings. Most eating places also very small and cramp.
If you think you will be outdoor a lot, then better prepare well. Once you are inside buildings or trains, you may need to remove the outer layer as you may feel (very) stuffy inside. Bottom line is, you want to be able to enjoy the winter, so don't play hero (if you know yourself can tahan or not)