Creasing in citrus is one of the million dollar questions…. The most recent research that was done on it definitely pinpointed the mineral nutrition of the developing fruit about 6 to 10 weeks after fruit set.  Research from 2 different groups came up with different elements as the lead factors.  Citrus fruit develops in a biphasic manner.  The first burst of fruit growth actually involves cell division in the peel tissue more than anything else.  This occurs roughly in the first 10 -12 weeks after fruit set.  It is during this time, it is believed, that transient nutrient deficiencies may lead to weaker cell walls that will be manifested as crease in mature fruit.  Following this time of cell division in the peel, then the juice vesicles begin to develop, and then the increase in peel as the fruit expands is largely due to cell enlargement.

Alternate bearing…. Another million dollar question.  We know that hanging the fruit late in the season will increase alternate bearing especially in citrus varieties that are prone to AB.  Maintaining overall tree health helps to minimize AB whereas sudden catastrophic natural events (freezes come immediately to mind) will worsen AB even when everything else is done correctly.  It is often difficult to snap a tree out of AB once it gets to cycling.

Waste decay; the main sources of decay in citrus is due to Penicillium decays.  These decays are WOUND pathogens so careful handling at all steps from harvest to the consumer will reduce the amount of decay.  Judicious use of postharvest fungicides that inhibit growth of the fungus or reduce sporulation will decrease decay as well later in the handling chain.  CAREFUL handling is of paramount importance and proper application of control measures.  If you are dealing with organic fruit then extreme care is your best defense plus judicious use of various fruit sanitizers in the packinghouse.

Rind breakdown can be cause by many factors… old fruit, rough handling, methyl bromide fumigation, prolonged cold storage.  Bottom line is to know your fruit and handle it carefully. 

As for irrigation I would consult an irrigation specialist from whatever area you are sourcing your citrus since local conditions very much influence how you need to approach irrigation.

Some good review resources for citrus postharvest handling are:

FRESH CITRUS FRUITS, available on Florida Science Source book distributors.  This is a great reference book.  Another good book is the APS manual on citrus production.  There is a very good postharvest chapter in this book.

                              —Mary Lu Arpaia