Did they run an infectious disease profile for blood parasites? They should check for Bartonella but Doxycycline is the treatment for it anyways, and if your cat is infected you would get a false negative if you were to retest now for it since she has been on doxy.
There are a number of diseases can be spread by fleas & ticks which is why flea control is important. Most of them are uncommon and usually do not cause many problems in cats that are exposed, but in a cat that is older and already may have underlying problems, it is not totally surprising to find that a blood parasite has taken over.
Doxy has a problem with causing stomach upset. I can not take it personally because it makes me VERY sick to my stomach and quite ill.
Capstar only stays in the system about 24 hours and Program is only for ONE month, not six! Also, both are oral medications. Capstar would have been my first choice for an oral medication but I would have probably used Advantage for a topical, NOT program, but there is nothing that can be done about that now.
What kind of canned food are you using? Canned food is VERY important for cats and should never be considered to be a "treat". That would be like saying water is a treat for you.. it is totally important for proper functioning.
Are you using something like Nutrical? They make some brands for older cats with extra vitamins and minerals for them.
Sorry that your kitty isn't feeling well. But to answer most of your questions, the answer would be "yes" to almost all of them... yes fleas can cause this kind of problem.. yes I have seen stuff like this happen before..
Hope she feels better soon!
My cat is smarter than your honor student.
Stop Dog Fighting ~ Neuter Mike Vick!
~ RIP Timmy ~ May 2009 - November 6th 2009