What is the correct "tense" that follows 'if' in this question, and the tense of the clause that follows next?

If he refuses to remove the instruction, it will confuse people.
If he refuses to remove the instruction, it would confuse people.

Correct, implication is that the instruction is still in the note and you are discussing whether or not he will remove it, presumably before it is used.

If he refused to remove the instruction, it will confuse people.
If he refused to remove the instruction, it would confuse people.

Correct if the note is already written, he had had some reason to know the instruction might be confusing, and you are discussing whether he has removed it already.

'Refuses' indicates something he might do in the future; 'Refused' indicates something he might have done in the past. 'Refuse' is incorrect in any case.

'Will confuse' is a declaration that something will happen; 'Would confuse' is a statement of something the speaker believes will happen -- there is not much difference between these, many native English speakers would (or will) make no distinction between them at all.