For one thing, it's not really a "bad habit" to use filler words. Natives (even highly educated natives) use them all the time.
It's only a "bad habit" in the sense that you'd want to avoid overly using them in formal situations or where you're expected to be a professional, but as a beginning learner of the language, no one is going to be holding you to the standards of an NHK newscaster or a Mitsubishi sales representative making a pitch to an important client.
On the contrary, dropping the occasional あのう, ええと, なんか, なんていうか, なんだろう, なんて言えばいいんだろう, etc. will make your speech more natural, especially if the alternative is just completely freezing in mid-sentence or subconsciously blurting out "Uh...", "Uhm...", or other English filler words.
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As for your larger question about when to pause and/or leave a sentence trailing off, unfortunately this isn't really a "simple question".
In fact, it's very hard to speak about in the abstract, because it can only come from a deeper understanding of the language and knowing how a native speaker would "complete" various thoughts.
Like, as an English native speaker, if I said any of the following...
"I've always dreamed of going to Japan, but..."
"Why, you little..."
"What in the...?"
...you'd be able to fill in the rest, I bet.
Maybe you wouldn't know exactly which words I was about to use, but the idea would be clear, right?
It's the same in Japanese.
It's not that Japanese people have some special kind of telepathy, it's just that they share the linguistic/cultural context to be able to know what might follow a certain thought/expression.
So I understand that this might not be a particularly satisfying answer, but the only way you're going to develop this intuition is by improving your language skills and listening to a lot of native Japanese. There isn't just a one-size-fits-all answer for "when do I pause" or "when do I not need to complete a sentence".
There are certain patterns that you may commonly see "ending" non-complete sentences, for example -て forms of verbs (e.g. どうしようかな~と思って, etc.) -(ん)だけど (e.g. 東京駅に行きたいんだけど…, etc.), -のに for contrary to fact wishes (来ればよかったのに…), conditional forms (行けたらなぁ…)but it's not as simple as "you can always do this when X".
The only real answer is, "when what you've said forms a meaningful utterance that will convey meaning to the listener."
And knowing what constitutes that will only come after you've developed a certain level of familiarity with the language.
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Sorry, that was kind of an essay. Hope it gave some perspective, though.
(For what it's worth, thank you. I feel like it's been a while since someone here was asking thought-provoking questions on the language.)