Hello.
1 and 2. Job DESCRIPTIONS are what are important, not the job TITLES. After all, an employer can call a job anything he likes, that makes sense for him within his organization. It's the skills you use in carrying out your job that INZ are required to scrutinize, to see that you are 'worth' granting a visa to. INZ have quite often been known to change the ANZSCO number on a visa application if they could see that another one was more appropriate than the one the applicant had picked on in the first place. I don't think the difference between what was on your current visa and what you put on the new one would make any difference. What's done is done, you have the visa, and if you, working the job now, have found that the other category seems more of a close fit, I don't think anyone could hold that against you. In any case, if INZ had any queries about this, they could be discussed and sorted out during the processing of the case.
3. Yes, you can use your manager's amplification of the original job description to make things clearer. In your place, I would put this in with the ITA. INZ will be contacting your employers in any case, as part of the verification about your job and the company, and they will probably, as well as sending a questionnaire, talk to you, and to your employer, to make sure that everything tallies. But having sent the 'correction' in the first place ought to save time and make things easier, by starting from the right place, not any wrong impression that might have been made by the basic job description.
4. That shouldn't make any difference. (There are many jobs in the financial and IT sectors which are held by people whose skills have been learnt by doing the work over years of experience, though their original qualification was in some other field. Such people can be AS qualified, if not more so, by that experience, than someone whose degree shows they've learnt the theory - that said with no disrespect intended to either side.)
5. All applications "in the pool" (submitted) before 12.59 p.m., fortnightly, Wednesday, with more than 140 points (or 100 points, with a job offer) will be selected. (That from ChrisMwn, an LIA who posts on this forum.)
6. No, you don't have to claim any points that you don't need, and given that you have a skilled NZ job already, you only need a minimum of 100.