It really is Wabun Code. The telegraph sequence at the start of the song was widely known and had been discussed on Japanese website, all of them says 「集｛しゅう｝ 愛｛あい｝してる」 (Shu-u, ai-shi-te-ru) is the encoded message.      
If you take a look at the Wikipedia page you cited, the small ゃ ya, ゅ yu, ょ yo in the digraphs are encoded the same as regular や ya, ゆ yu, よ yo.
So we can comparing your attempt at decoding:
-•-• -••-- •--
and the supposed coding of the message (shi-yu-u):
--•-• -••-- ••-
Listening to the telegraph sequence again to cross-check, while I can agree with Japanese fans' transcription of the 3rd mora
••-, I could only hear 1 dash at the beginning for the first mora
--•-•. And apparently, the author of answer  on Yahoo also encountered the same problem:
ただ、最初の音(？)が微妙に「にゅ」と解読されるようですが、「にゅう あいしてる」だと意味が通じないので「しゅう あいしてる」で間違いないとおもいます。
This is going to be a spoiler,
but it seems to be "Shuu, I love you".
"Shuu" here is referring to Ouma Shuu.
However, although the first sound somewhat decodes to "nyuu", "nyuu aishiteru" doesn't really make sense, so I think it is definitely "Shuu aishiteru".
There is this question on Yahoo Answer which says that apart from the Morse code at the beginning and at the end (which I myself also confirm, but I don't bother to decode it), the asker feels that there are also Morse code playing in the background through out the song (which I also feel there is something, but listening closely reveals nothing).