As is said elsewhere, at a thread about Greek pronunciation, we can’t know such differences, so that, whatever way you choose to count the length will be arbitrary. Instead of that, just use modern Greek. If you notice your pronunciation carefully, you will see that you yourself in modern Greek pronounce some syllables longer than other. To learn the grammatical length of syllables, go to polytoniko.gr, where you will find also the rules to write in polytonic Greek. Search the web for an answer-book on Pharr; you can also post here questions about chapters that make your life difficult.
You chose a great way to start. As you progress with Pharr, you can start also reading a complete translation of Homer in English together with the original and observe differences. This will make you more sensitive on what can not be translated. Don’t neglect etymology. When you feel more comfortable with homeric Greek, read Elpenor’s second and third lessons, which are based on Homer and will give you some help on how to interpret and translate.