I'm afraid you might have to run twice, once is for submitting the documents for your applciation, another is to get the visa when it has been approved.
The usual place to go for this kind of applciation is the immigration office in Putrajaya. But why don't you contact the State Immigration Office and see if they could process it there?
There is a list of offices in Johor on the immigration website, www.imi.gov.my
and find the nearest one to you.