We often travel to Japan around that time, and will be this year as well. We are from Melbourne, Australia, but Ifve lived in London, so understand the temperature stuff.
The trick, you got it, is layers..LAYERS....
I doubt you will need any major thermals, so the 1 pair tights is fine..Forget the tweed coat: it will be a heavy and annoying encumbrance.
Everywhere in Japan is super-heated: trains/hotels/buildings (shops etc ) are strip-off territory. And sweatboxes.
I always wear a singlet, (?vest?) polo or T-shirt, medium weight zipped hoody, comfortable walking pants (Skirts and I have a poor relationship for walking, due to the shoes needed...) good socks (because you take your shoes off all the time and people see the socks..) and comfy walking shoes: need to be VERY comfy: preferably easily removed, as laced up shoes are a pain to take on and off all the time (which, as i said, you do, all the time, in Japan: temples, some smaller museums, restaurants etc ): so if your Merrills are the zip ones they will be perfect (its actually what Ifm taking this time)
We carry day packs, complete with cap (we are sun conscious here, so tend to put on a cap at the slightest hint of sun....lol) beanie (if cold) scarf, and mittens, if we go somewhere we know will be colder, like Mt Koya. And we shed layers into the day pack at regular intervals.
And finally, a good RAINproof, not SHOWERproof, rain jacket, that folds up easily, and also can be a windbreaker if needs be.: so your 3: 1 should be fine.
Also, remember, in Japan, you walk: a lot: so unless you are standing still for any length of time for whatever reason, you will be comfortable.
Leather boots for walking around cities could be a bit hard on the feet: you really will walk a huge amount....even if you think you are gjust doing museumsh, you will walk an age to get to them: trains donft stop right at the museum entrances, believe me.
Dont forget websites have maximum and minimum temps, and average temps: minumum will be overnight,
Maximum will be well during the day, when you will be out and about more active.
http://www.data.jma.go.jp/obd/stats/etrn/view/monthly_s3_en.php?block_...is a good site: you can alter locations and data parameter.
You arenft really going high into Alps: you probably wonft even see snow on the ground : the only snow-on-ground we have seen at that time was early April, in Sendai, which is way north of your itinerary, and it was just a small flurry, and more like slush.
We are planning on weather being cool in the mornings when we set out, and warmer in the day when we are active, then cooler in the evening.
If you are taking dressy outfits, remember, you only need one: the other half can cope with you wearing the same thing more than once, and no one else will know......
Collapsible layers that compress easily and are not a pain to lug around will be your friend. Comfort is essential: fashion less so, but I do agree with liking to look nice, not untidy.
Good luck!!!