There are a number of Japanese words which have distinct compounding forms:

  * -a/-e alternation: 天・雨、酒、上、風、目 — many examples.
  * -u/-i alternation: 神（[神]{かむ}[集]{つど}ふ）、月（[月]{つく}[読]{よみ}）
  * -o/-i alternation: 木（[木]{こ}の[葉]{は}）、火（炎【ほのほ】）
  * -a/-o alternation: 白（[白]{しら}[雪]{ゆき}）

[This BBS
post](http://jbbs.livedoor.jp/bbs/read.cgi/study/10958/1283085223/18) has more
examples. There is also another kind of alternation I know of, even rarer:

  * s-insertion: 雨（[春]{はる}[雨]{さめ}）、青（[真]{ま}っ[青]{さを})

I have three questions:

  1. Are there any other alternations I have missed?
  2. Is there an exhaustive listing of words with exceptional compound forms somewhere?
  3. To what extent is this process still alive? For instance, [風]{かざ}[車]{ぐるま} is a comparatively recent coinage.
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etymology history phonology compounds irregularities-exceptions
Exceptional compounding forms
1) I don't think that you have missed anything or that you should really be
concerned about it too much. Even without exhaustive research, people who know
a lot about kanji know that these readings stand out as being special. Perhaps
one of the readings is used in two, rather than just one word, but the sound
would still seem unique in comparison to the variety of words used with the
other readings. So, I hope my 90%-sure "yes" can set your mind at ease?

2) [This
link](http://ja.wikipedia.org/wiki/%E7%86%9F%E5%AD%97%E8%A8%93#.E4.BE.8B) goes
directly to a page with a list of kanji with readings that appear exclusively
in one word.

3) Are words like this still being created? Yes. To what extent? That's a more
difficult question. People are still doing it quite often for names, and I
imagine it happens with some frequency as new words are created to describe
things (e.g., in science). It's hard to quantify, especially because I wasn't
able to uncover a list of 'new words' in Japanese.
日本語の新しい言葉/日本語のつぐに作った言葉とか.... These google keywords don't turn much up, but
I'll try to be more creative for your cause and do a little more searching....
Anyway, I hope it's sufficient to say 'it's not a dead practice'.

It seems to me, the reason people use these "distinct" readings is because
they're easier to say. I think some strange English sentences are thought of
in the same way. You can tell by saying tongue twisters. They force your
cheeks to go in-and-out, or your tongue to thrash to-and-fro in such a
meticulous manner. For strange English sentences, saying them normally has the
same effect. In Japanese, try saying "MOkuNOha", then "KInoHA", and then try
saying "konoHA". The upper-case indicate open cheeks, and the lower-case
indicate closed cheeks. It's easier to move your cheeks from in to out, rather
than out, to in, to out, to in, so I think we just elect this simple
variation.
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As I commented earlier, I am pretty sure that much of these alternations are
due to phonological rules. I realized that, among your patterns,
a/e-alternation and u/i-alternation follow naturally from assuming:

  1. 露出形 vs. 被覆形 alternation hypothesis (which you also mention) as in my answer in [Why is a place that sells さけ a さかや?](https://japanese.stackexchange.com/questions/3533)
  2. The phonological rule described in my answer in [What does こまけー mean?](https://japanese.stackexchange.com/questions/3746)
  3. The long vowel mentioned in 2. above was shortened.

However, this does not explain your o/i-alternation and a/o-alternation. This
fact suggest two possibilities: (1) the underlying verb is of somewhat
different quality, and assuming an appropriate underlying vowel, these
alternation actually fit the rule mentioned in 2, or (2) there is another rule
in addition to the one mentioned in (2).

To the extent that this theory is correct, it predicts that there can be
o/e-alternation such that in compound forms, ends with [o], and in isolated
forms, ends with [e].
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