If you ever have any question about whether or not a lacto-ferment has gone bad or not, test the pH. You can get test paper for cheap and it will show you instantly the pH. In general, anything below 4.5 is okay, in my opinion around 3.8 is ideal. I don't think a 100% diet of really acidic (3.3 or lower) fermented feed is ideal, I think it's too acidic. I think they should have some unfermented feed or at least from free-ranging time where they will get some unfermented items. Could you imagine eating a diet of 100% very sour foods?
I use this pH paper:
http://www.ebay.com/itm/Hydrion-Mic...895637?pt=US_Garden_Tools&hash=item3f3cbc08d5
But since your feed smelling incredibly sour, I would bet money that your pH is plenty low. Smell can tell you a lot, but I found the test paper very helpful at first when I doubted my nose. Above 4.5 and the likelihood of of "bad bacteria" thriving and populating increases and below that it decreases. Most of the studies of FF I have read have used a pH of 4.5. As the pH drops, the chances of "bad bacteria" even existing anymore decreases big time. The acidic nature is not hospitable to the bad bacteria and the lactic acid bacteria also destroy them.
So to answer your question, no, I doubt you've got bad germs in the 2 month old batch, but the nutrition will degrade after a while, especially the proteins, as they get consumed by the good bacteria. You could mix in some sort of protein item into the batch to boost the protein while you use up the batch. Perhaps next time don't make as big of a batch so it get's used more quickly.