This is nothing to do with grammar - it's a phonological phenomenon, and connected to the fact that pronunciation in English has changed much faster than spelling .
First of all, the -gh. In Middle English this was pronounced as a velar fricative - that's the sound spelt "ch" eg in the Scots word "loch" or the German "ich". It's phonemic symbol is /x/. However, gradually this either changed to a /f/ sound (eg enough, cough, laugh, bought
) or was dropped all together ( eg though, through
Then the vowels. If you take "through" - in Chaucer's time there was no standard spelling. It could be written thurgh, thorgh throgh through thorogh thorough
. Gradually the written language became standardised and by Shakespeare's time "through" had settled to either through
. During this time though, what is known as the Great Vowel Shift was happening - vowels were changing quality. How this happened is very complex - this
is an good site if you want the details.
But as I said, although the pronunciation of both the vowels and consonants changed, the written form didn't. And we've ended up with words whose written form actually reflects a much earlier pronunciation, which was radically different from the modern pronunciation.
So - nothing to do with grammar. The "rules" are phonological - but unfortunately they're those of the phonology of the 13th to 17th centuries