Hmm, interesting.. yeah the whole い being left out never bothered me except at when I first saw it with a verb whose dictionary form ended in つ because then it was hard to tell if it's the potential form or not. e.g. 待ってる ("I'm waiting") and 待てる ("I can wait") and at the time I couldn't remember if the potential form had a っ. Anywho, I've always thought of the contraction of the い sound similar to the colloquial loss of the final 'g' in english progressive forms, e.g 読んでいる-> 読んでる is similar to "I'm reading" -> I'm readin'
I could maybe put in a parenthesis the omited い like what I did when the girl says 起立, she omits the つ so in the romaji subs I wrote "Kiri(tsu)" so I could do it like this; "鳴って (い)る" or do the parenthesis just make it more confusing? Haha.
Sorry for how slow I've been, my computer has been crapping out on me D: