I'm still trying to get a handle on the bloodwork/urinalysis issue. Did you watch the blood draw when the blood sample was obtained? If not, is it possible that a urine sample was obtained when they drew the blood sample? Were you charged for a urinalysis? (check your invoice.) There has just got to be a miscommunication here.
Did Bubba receive a complete physical exam when you saw your vet? The signs that you have described seem very general and non-specific. They may or may not be associated with urinary tract problems. I understand from your post that Bubba mainly seems less active and responsive than previously. A full geriatric exam (If he hasn't had one recently) might reveal a better picture of Bubba's present state of health.
My take on this is that you should have an open and honest discussion with your vet (or a knowledgeable technician in his office) about your worries and about Bubba's home care. Ask him to explain thoroughly what tests he ran, what those tests results indicated to him, what his diagnosis is, and why he thinks that Bubba needs antibiotics and special diet.
Be sure that he is fully aware of all herbal meds that Bubba receives and of Bubba's specific home diet. Explain your feelings about the use of pharmaceuticals and commercial diets.
Let him give you his opinion on why he seeks to change the diet or prescribe certain meds.
He might have some compelling reasons.
If, after all this, you still don't feel confident about your vet's recommendations, and if you still feel that Bubba is not acting 100% normal, you can always seek a second opinion. This is done all the time, and should not upset your regular vet. Sometimes another vet is better at explaining things, or they might pick up on signs that the first vet did not see.
If you do decide to seek another opinion, it would be helpful if you had copies of Bubba's recent care, lab work, exam findings and recommendations, etc. If you could take a list of your concerns and observations, this would also make for a more efficient consult, with less danger of forgetting something until after you are on your way home. (By the way, you are entitled to a copy of your pet'srecords, but the vet is required by law to keep the originals, so don't expect the original documents from your first vet. You do have the right to have all the information in the records, either as a xeroxed copy or as a paraphrased copy. The vet also has the right to charge a small fee for this service.)
Back to the issue of medication side effects: yes, some meds might make some animals nauseated. However, the ones affected might be as few as 5 or 10 percent of patients receiving the drug. That means that 90 to 95 percent do not have any problems, but only receive the benefits of treatment. It is important to keep things in perspective, and not throw the baby out with the bathwater! Everything in medicine is based on comparing benefits vs. risks. The reason we consult doctors and veterinarians is because they have received the special and rigorous training needed to take all factors into consideration and help us make the best decisions for preserving health. Of course, we have a right to have our opinions on what care we will accept, but we don't always have all the information needed for making the best decision.
It doesn't sound to me as though anything you have done has endangered your pet's health at this point. However, if you have the impression that something is just not right with Bubba, I hope that you will follow up on it and seek answers, since delay in treatment can sometimes lead to unforeseen problems.
You asked about a fecal color change since you have begun the home diet and homeopathic supplements (do you mean the cranberry tabs and the echinacea/goldenseal, or are there others?) This is probably not significant, and may be due to dietary change more than anything else. You mentioned that you are cooking for Bubba. Do you feed the exact same recipe every meal, or are there frequent variations in the ingredients? As a general rule, animals do not do well with sudden dietary change. It is usually best to allow a slow transition from one food to another over a 10 day period to avoid digestive upset. BUT, since I don't know all the facts about Bubba and his diet, it would be impossible to give you a "diagnosis" for his fecal changes. Be sure to discuss this with your vet as well.
Good luck, and keep me posted. I have to admit that I am very curious about the blood struvite thing! I hope things improve for you and Bubba soon.