Switching between pronunciations?

I started learning ancient Greek a few months ago using modern pronunciation, but the vowel merging of all the diphthongs and homophones were very frustrating so I started to use classical pronunciation with rough breathing, long and short vowels as well as keeping the diphthongs. However, besides liking the sound of modern pronunciation more (and the fact that I am planning on picking up modern Greek too), I am an Orthodox Christian and thus with classical pronunciation I am separated both from the current majority (liturgical or otherwise) use of Koine (for listening practice) and most of the content I want to read was already written at a time pronunciation was much closer to modern than classical pronunciation. So I feel torn between making the language easier to learn by having it be phonetic vs learning the spelling of each word individually. I also would like to use it (online for now) as a spoken language, insofar as possible for pedagogical purposes, but I don’t know if modern pronunciation will hinder me with that since most “speakers of ancient Greek” probably don’t use it. Anyone have any advice?

Well, you can’t have your cake and eat it. For what it’s worth, I met some Greeks who use the “classical” pronunciation when speaking ancient Greek. They manage it alright.

If using the reconstructed pronunciation helps you to learn, I’d say go with that. You can always change back later on.

How do you switch back and forth without spending an excessive amount of time re-memorizing the pronunciation of each word?

You wouldn’t have to re-memorise anything, as you’d just apply the rules of modern Greek pronunciation - so any time you wanted to make the long /o:/ sound of omega you’d change it to the short /o/, the /y/ of υ would always become /i/ etc. It’d be like an actor imitating an accent - maybe hard to maintain at first, and you’d slip up quite a lot, but not impossible.

And if it really is too hard to change, you could just stick with the reconstructed pronunciation.

In my opinion, it is not too difficult to switch from one pronunciation system to the other; I have recorded here https://vasilestancu.ro/TK/audio_library/switching_between_pronunciations.html a short passage (1 John 1:1-7) using two pronunciation systems (one which I am applying to Ancient Greek and one using the modern pronunciation). My problem would be whether one system could be an appropriate solution for both modern and ancient texts, but when I encounter combinations like this, for instance, μακάριοι οἱ εἰρηνοποιοί (Mt 5:9), with so many ‘ee’-sounds in so close sequence - and there are many such instances, I feel somewhat reluctant applying modern pronunciation to ancient texts with no ammendments.

When I was in Greece in Selianitika at the Hellenikon Idyllion, I went to the local Greek Orthodox church. I had the distinct impression that sometimes the priest pronounced η /ɛː/. Maybe to avoid the same problem?

If you use modern pronunciation when you speak ancient Greek some forms and words (especially in certain sequences, as has been pointed out) will be incomprehensible. You will either have to adjust your vocabulary and grammar or tweak the pronunciation (e.g. as bedwere describes) where it is necessary if you want anyone to understand you. I would have gone with switching between pronunciations in your situation, but I don’t like modern pronunciation any better than ancient, so that may make the choice harder for you.

I think this is what Luke Ranieri was trying to address with his Lucian pronunciation. It uses the consonant sounds we associate with modern, but uses a greater variety of vowel sounds and preserves quantity. It’s intended to be useful for pedagogy and poetry while being intelligible to someone who uses the modern pronunciation. See https://www.youtube.com/watch?v=ponGrCwjYWo