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#1. I guess, you are referring to the problems that you are encountering while loading GL COA. You may log SR against GL to know more details on how API loads data to instance. DELETE is a specific requirement in your case and I would suggest you to work with GL team and they may provide some solution or workaround to overcome this performance issue.
#2. No, concurrent program does good amount of pre-processing that you would not get if you directly call the java classes.
#3. Not sure, what you are exactly looking at. Are you looking for user guide to write your own iSetup API classes?
11i.AZ.H has got good amount of performances fixes overall and it is recommended release on top of 184.108.40.206CU. I would suggest you to upgrade to 11i.AZ.H.
Specific to GL COA issue, I don't think 11i.AZ.H would really help you much. It is very much functional issue with respect to API and you have to work with GL team to get workaround/solution. This may involve customizing the API according to your requirement.