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Please tell me which is/are incorrect in each number and which are/is most preferred in each number:

1a) It is not this, but it is that.

1b) It is not this, but is that.

1c) It is not this, but that.

2a) It is this, but it is not that.

2b) It is this, but is not that.

2c) It is this, not that.

3a) It is not this, rather it is that.

3b) It is not this. Rather it is that.

3c) It is not this, rather that.

4a) It is not this, but rather it is that.

4b) It is not this, but rather is that.

4c) It is not this, but rather that.

5a) It is not this, instead it is that.

5b) It is not this. Instead, it is that.

5c) It is not this, instead is that.

5d) It is not this, instead that.

6a) It is this, rather that.

6b) It is this, rather than that.

6c)It is this, instead of that.

Thank you!
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I assume "this" and "that" are placeholders that you intend to replace with longer phrases? Could you give an example of the sort of substitutions that you are envisaging?
Comments  
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I would probably only use the abbreviated versions with smaller phrases, so you can assume the placeholders stand for, say...

It is not the crowd who go wild, but the players on the field (who go wild/do).

Well, any noun phrase really Emotion: smile

It is not a car, but a truck.



The underlined words were not a mistake, but an intentional mispelling.

It is not the people who motivate us, but the brains within us that do.
I don't have much confidence in making general statements about many of these without going through numerous possibilities for "this" and "that" separately, which would be a long and arduous task. So, I just chose the car/truck example.

The choices within each group do not always have exactly the same shade of meaning, so it's not always as simple as deciding "which is preferred".

1a) It is not a car, but it is a truck. -- Possible; in the most likely interpretation the second "is" would be emphasised, suggesting that a car would have been ideal but a truck might do.
1b) It is not a car, but is a truck. -- Seems less likely than 1a.

1c) It is not a car, but a truck. -- OK.

2a) It is a car, but it is not a truck. -- Possible. Suggests you need a vehicle with truck-like capabilities, but this isn't it.
2b) It is a car, but is not a truck. -- Seems less likely than 2a.

2c) It is a car, not a truck. -- OK. This is the simplest and probably commonest of all the choices.

3a) It is not a car, rather it is a truck. -- Possible. "rather" is more formal and less conversational than than "but".
3b) It is not a car. Rather it is a truck. -- Possible.

3c) It is not a car, rather a truck. -- Doesn't seem very natural.

4a) It is not a car, but rather it is a truck. -- Doesn't seem very natural.
4b) It is not a car, but rather is a truck. -- Doesn't seem very natural.
4c) It is not a car, but rather a truck. -- Possible.

5a) It is not a car, instead it is a truck. -- Comma splice.
5b) It is not a car. Instead, it is a truck. -- OK.
5c) It is not a car, instead is a truck. -- Ungrammatical.
5d) It is not a car, instead a truck. -- Ungrammatical.

6a) It is a car, rather a truck. -- Ungrammatical.
6b) It is a car, rather than a truck. -- OK but I would not use a comma. A common form of words.
6c) It is a car, instead of a truck. -- OK but I would not use a comma. Suggests that you were expecting/wanting a truck but got a car instead.