Ammonia is not present in the urine if it is taken within 15 minutes after evacuation. Ammonia is only present in aged urine. Aged urine is even more beneficial for exterior use (massages, compresses). As for the acidity, yes it is not advised to put back in the body more acidity and that is why what you eat is so important.
Armstrong http://naturinologie.info/ressources_amazon_en.htm#Water_of_Life who treated many patients suggested taking everything that passes. He helped cure lots of people (desperate cases) this way. But as advised by authors, we should always prepare a long time in advance eating lots of alcalinizing foods a few weeks before starting a fast or the therapy. We can monitor the situation with ph strips. Massages, enemas, compresses, injections etc. can complement the internal therapy. Massages and enemas are a must with a fast.
Sorry if my english is a bit raw. It is not my mother tongue.