>What is the difference in pronunciation between the word него & the phrase не го
There's no difference. Though there can be a difference where the stress falls, depending on the following word.
>Likewise, how can you disambiguate нѐ сакате (нас) and не сакате?
Again, there's no difference in pronunciation. In fact, the diacritic over the first нѐ, exists solely to separate the two meanings. It can be confusing at times even for Macedonians, but usually there's no problem thanks to the wider context.
>And which is best: не нѐ сакате нас, не ни сакате нас, or не нас сакате?
Hе нѐ сакате нас? - This is the only correct form. The others are wrong.
Stress can vary between dialects. In standard Macedonian there's this thing called "акцентскa целост" where more than one word sort of combine and basically act as one word when stress is concerned.
So, in the phrase "Не нѐ сАкате", the stress falls on the antepenultimate syllable (the third counting from the last). However, if phrase was "Не нÈ сака", then because of the "акцентска целост", it falls on ѐ (still the third syllable from the end).
As I said, this is only in standard Macedonian and some Western dialects, so don't be surprised if you hear "Не нѐ сАка" from someone in the East. :)
>I prefer to use ни instead of нѐ due to the confusion at both не's occurring at the beginning of the phrase.
Don't do that, ни has another meaning.