Apostrophes were once used in a lot of plural cases (I've said more on this [here](http://english.stackexchange.com/a/104235/15770)) and while some such cases are now completely obsolete, some are still used to varying degrees.

The case of pluralising a single letter is perhaps the strongest survivor of the pluralising apostrophe (and indeed even in the case of pluralising letter grades, as despite your claim one can indeed find "She got five A’s and two B’s" and similar uses today). It avoids a tendency to consider the forms *ts* as a word and even more so *is*, since there of course is already a word *is*. (Also the English words *as* and *us* and abbreviations like *vs*).

So, considering that apostrophes for plurals perhaps shouldn't stick in your craw *quite* as much as it does, (i.e. fine as a personal preference, but not "incorrect"), and considering the various points you've made, there's no perfect answer as to "which is it?" and all three are found in different styles of correct contemporary use.

I'd add the possibility of italicising the letter:

> I just need to go through it once more to dot the *i*s and cross the *t*s.

Which is my personal preference when markup is possible, but not the sole "correct" choice, either.