There is no setting for the minimum withdrawal amount for custom coins, since these coins cannot normally be withdrawn (or deposited). If you have developed your own mechanism for withdrawing/depositing such coins, then this is where you should be checking the withdrawal amount against any limits you want to place.
Moreover, the available balance is not related to this. Available balance is the part of the user’s balance that is not currently locked in pending transactions or in market orders on the Exchange extension. This is not a feature that you can control; rather, user balance is split into “available” and “unavailable” to guard against double-spends.