I have set up an Agricraft Farming Station to control the plating and harvesting of my Capacitor Seeds/Plants, the Harvest Unanalyzed Plants module, Seed Multiplying module, and the Seed Analyzer module all work(manually bread to 10 10 10) I have gotten my farm full of Mature plants, however, it is not harvesting them, and my hoe is taking durability loss like it is.

Check your config file, is "seedsAutomaticHarvestingEnabled" set to false? (that's the default)

Ok it is a balance issue, I wasnt sure if it was supposed to and wasnt but it is not supposed to

Yes it is. However, now that I think about it, it seems I forgot to mention that restriction somewhere in the seed description. Sorry.