oh, ghosty - re: cough, through and though
These are tricky ones, admittedly, and I would deal with them especially, but they are not impossible and still follow some logic.
'gh' is often used to spell the 'f' sound as in cough, rough, trough and laugh. Normally, I would only teach this final consonant once the vowel spellings were known, but these are so infrequent they might as well be taught at the same time. So, cough and trough would go together as on these occasions, the 'ou' both represent the 'o' sound, and then laugh and rough would have to be separate. I would probably display the words with the approprite JP picture reference above the vowel letters just to reinforce those.
'though' has two sounds: th+oa. the 'th' is regular but the 'ough' for oa is not. I think this is alone in its sound/letter representations, so it would have to be learnt alone and I would probably display it with the appropriate JP picture above the 'ough' again.
The same with 'through' in teaching it: it has 3 sounds - th+r+oo where 'ough' is used for 'oo' and right now, I can't think of any other words that do it.
English is a very complicated language as our words come from so many historical sources, but as most of these original languages also have a phoneme representational source, they are all phonically decodable, albeit with a huge veriety of spellings for each sound. But, this does not make English non-phonetical or too irregular to teach systematically. What it means for me is that it is more important to teach it systematically so avoid confusion.
As long as children can hear that spoken words are sequences of sounds, and know that these sounds have letter representations, be it one or more, and are taught blending skills, then all they need to be taught systematically is all the representations for these sounds. Of course there will be some words that need to be taught separately - and I think we have found some!
It is the limited, ineffective 'traditional' phonics of 26 letters = 26 sounds that renders 'phonics' teaching virtually impossible.