Best way would be approach the company and talk to them. Give a formal letter of resignation. This is to ensure that your name is clean.

As for the payment, you can always negotiate with the employer being the fact that you were not paid earlier before you MIA. Hence you may just need to top up the balance.

Yup. Violation of contract is a point. However, employer also have duty to pay employee for the job performed in the past.

However if case is brought to court may involve more than RM2000 , i.e. interest charges, time needed for employer to find replacement, loss of hours etc. All would definitely cost more than 1 month salary.

Do your best to negotiate. You may need to put up with some pep talk but remember it is your fault in the first place.