They're fine as is, or fine without them, as Maulik noted. If you're looking for alternatives to diversify your use of English:
What are you doing? I mean study-wise.
- What are you doing, study-wise?
- What are you doing in terms of studying?
- What are you doing as far as studying goes?
- What are you doing to study (for the test)?
That last one sets up a lot of possibilities: "How are you planning to study," "What kind of studying are you doing..." I won't bother listing them since you seem to be asking for drop-in alternatives rather than all the ways you could rewrite the sentence.
So that is the case! I mean he used to go there, right?
Not entirely sure of the context you are imagining. Alternatives might vary based on the situation you were thinking of. Here are a few:
- So that is the case! I thought he used to go there!
- So that is the case! Didn't he go there often?
- So that is the case! That he went there often?
- So that is the case! Like, he went there often? (this is a casual usage, usually associated with west coast English)
- So that is the case! In regards to him going there?
...that last one wasn't great, but you get the idea. Your use of "I mean" in your second example is just about restating the topic of your conversation.
You will see a lot of these in action if you can get access to a live talk television. They don't appear as often in writing or scripted television, but they happen a lot in spontaneous speech.