I’ve always been told that the body should be alkaline; here, I am told to keep the colon acidic to improve intestinal flora…where is the balance?

The body pH and intestinal pH are two totally different things. 

The optimal pH in your gut is between 4.5 and 5.  A healthy flora maintains this when it is producing sufficient amounts of lactic acid.  When the flora is compromised, the level of lactic acid drops and the pH becomes more alkaline, favouring the growth of harmful bacteria and Candida.  Lactic acid is essential for the assimilation of alkaline minerals. 

In short: the more acidic the bowels, the more lactic acid there is, the more we assimilate our alkaline minerals and the more alkaline our BODY becomes. 

The opposite is also true: the more alkaline our bowels are, the less lactic acid there is, the less we assimilate our alkaline minerals and the more acidic our body becomes.