oh man, this week has been insane. schedules changing almost every day with anti-virus measures in Japan. sorry I’ve been so MIA with this puzzle.
will hopefully have a noodle on it tomorrow, if we manage to have a quiet day. this seems like exactly the kind of puzzle I’d really enjoy in English, but we’ll see how far I get in a second language. 
3-across ノドゴシ
1-down サユウ
5-across マメタン
3-down ノロマ
4-across ロウ
We’re actually more than half finished…
Aha
27-across メイロ - Sadly, that makes ユソウ incorrect for 31-down…
20-down アテ, I guess?
20-across アシドリ
31-down リクロ
29-down イッタリキタリ (honestly, this kind of abstract clue is impossible to solve unless you’ve got a fair idea of all words that it could be.)
22-across ギョタク
32-down クブン
23-across ダイキン
Edit:
Ok, worked out 28-down thanks to Google. 薩摩守 is a slang term for getting a free ride, or in other words, 無賃乗車 - which is to say, the answer is ムチン. Basically, 薩摩守 is somehow related (my Japanese-fu isn’t strong enough for me to work out the precise relation… some kind of official title, perhaps?) to 平忠度 (たいらのただのり), and ただのり sounds like ただ乗り = free ride
More info:
Anyway, that makes 28-across ムリツ
And now there’s only 25-across (and 24-down) left.
24-down ミエ（見得）
a kabuki term referring to the poses struck by actors in scenes at key moments
which makes エン the start of 25-across… perhaps meaning as in circle? going round and round type thing? but i am perplexed with the ツ ending. TT_TT
Ok, this has gone on long enough, so I looked up the last one - it’s エンピツ. I guess from the practice of standing a pencil up on end, letting it drop, and then going in the direction it points? I’ve only ever seen that done with sticks, though.
Next!
Lots o’ kanji clues in this one. Not even sure what to make of some of them. And that’s a lot of characters in the super secret magic word.
To start off with:
4-across カナ
10-down シメナワ
11-across…メガ? Though if we’re talking SI prefixes, that should be 百万倍 
13-down ニクジャガ (Had to research that one. Learn something new every day.)
18-down タマゴ, I guess.
シロミ, more likely. Meringue doesn’t include any yolks, just the whites. (Watching baking shows coming in handy now–never made a meringue in my life! Heh.)
Still reading this thread but rarely finding the time to sit down and look at some clues.
17-across ツララ
22-across サラウドン
This probably makes 34-down ドライブ
How are you so well-read on Nagasaki cuisine? 
I’d say so. Seems to be a thing in Japan - just going for a drive as a hobby. Nadeshiko’s sister does it in Yuru Camp, even to the extent that she’s perfectly happy spending half a day driving Nadeshiko to the middle of nowhere.
Ah, of course. Which makes 3-across クシャミ. Is… is there a comma omitted from the clue? Is that why it seems to make no sense at the beginning?
I knew meringue is made from egg white. It just didn’t occur to me that that would be the answer.
1-across モツニ
8-down ツツ
Makes 9-across ツクシ, which I’m not sure I quite understand.
I was confused by the 羊歯 too, but 羊歯植物 or シダ植物 is a classification for ferns. The clue is asking for a plant that grows the most in the beginning of spring and is also classified as a シダ植物, and つくし seems to be one of those.
Living close and visiting recently 
Nagasaki 名物 can be either ちゃんぽん, カステラ or 皿うどん, and only one of those is crunchy
1-across モツニ (I just saw you already had that)
6-across イコツ maybe?
33-down オチ if I’m thinking of the right term
Nah, there’s specific terms when it comes to yon-koma - the four panels are ki-shou-ten-ketsu. It comes from classic Chinese poetry, which always amuses me. ケツ is the answer here.
21-across カジカ (cause it’s 鰍, see?)
24-down ジガ
25-across ガスケツ
29-down カスミソウ
The super secret magic word almost certainly starts with クロスワード. But then what? パズル? ブック?
14-across ジロン
15-down シュッパツ (which I should have spotted ages ago)
Which makes the super secret magic word クロスワードパズル
Which means I can jump over to…
27-down ノズル
27-across ノンブル
31-across コイ
31-down コンクール
28-across ルーク
23-across シズク
I figured you guys might need some help
5-across イワシミズ
6-across イコツ
7-across シンパク
16-across ユミ
19-across コース
26-across クソ
32-across ルロウ
4-down カイカイシキ
12-down コン
19-down コミミ
20-down クラ
22-down サーズ
26-down クラス
36-down クロ
38-down ルイ
Heh. And where have you been hiding?
I picked up the book several times intending to get more done, but I actually did any. I’ll have to sort though those answers in the morning, though…
umm… 社会距離?
カソ, if you please. Thought you’d sneak a swear word into my crossword?
To wrap it up, then:
35-across ラク
37-down ネットバンク
2-down アク
10-across アイコ
13-across サンソ
37-down ゲカ (?)
Hvat is the first character in the clue for 3-across?
19-down イト
25-down ヤキモチ?
28-down ツナミ
36-down エサ?
19-across イワナ?
24-across シンガリ would be my guess but it clashes with @Heiopei‘s ゲカ
29-across ミキサー but I‘m not sure if you’re supposed to put ミキサア?
