Justy,
Your symptoms and prescriptions sound exactly like what I went through for years, including pneumonia!
What happened to me was that the long term unidentifiable stomach issue suddenly went away after the antibiotic I took for the pneumonia (10 days of, I believe, doxicycline?). But that stomach problem STARTED with an antibiotic (Flagyl) and the prilosec and imeprizole really wrecked me and probably created the overgrowth that the antibiotic then dealt with . . . years later, after suffering with it forever. It was really an eye-opener.
My stomach has never been normal again. Today I've found that probiotics are very helpful, also -- possibly -- for my mood. I notice that when my gut gets messed up I get paranoid and depressed. High doses of probiotics have been shown to improve mood (many serotonin and other receptors in the gut). I take Jarro-dophilus +FOS 3.4, 3x a day. For a long time I didn't take them because I'd tried one once and my stomach went crazy, but years later, I gave it a go again and it was fine.
After I could no longer tolerate the pharma drugs, what I found worked a lot better when my stomach was really bothering me was Slippery Elm -- I would get the bark at an herb store and soak it overnight and then sip the viscous liquid throughout the day. It worked far better than anything from the pharmacy to just soothe my stomach.